Posts Tagged ‘Complementary DNA’

Understanding of OVO-like proteins (OVOL), which are members of the zinc finger protein family, serve as transcription factors to regulate gene expression in various differentiation processes and are involved in epithelial development and differentiation in a wide variety of organisms. Thus, comparative genomic analysis among three different OVOL genes (OVOL1-3) in vertebrates may shed a light onto this crucial gene for development of molecular diagnostics and targeted therapies.

The Figure is from:

Genomics. Author manuscript; available in PMC 2010 June 29.

Published in final edited form as: Genomics. 2002 September; 80(3): 319–325.

Analysis of mouse and human OVOL2 gene products. (A) The 5′ end sequences of the mouse Ovol2B cDNA and the deduced OVOL2B protein. The “#” symbol indicates the position of an internal methionine previously mistaken as the initiation codon [14]. (B) Deduced amino acid sequences of OVOL2A proteins in mouse (mOvol2A) and human (hOvol2A). The “*” symbol indicates amino acid identity. The four C2H2 zinc fingers are underlined. The predicted NLS sequences are boxed. Sequences common to mouse OVOL2A and OVOL2B start at the brackets in (A) and (B). Human OVOL2B starts at the internal methionine (bold). Shown in bold and italics are positions where our predicted sequence differs from the previously reported sequence [14]. (C) Phylogenetic analysis of OVO proteins. cOvo, C. elegans OVO (GenBank acc. no. AF134806); dOvo, Drosophila OVO (GenBank acc. no. X59772); mOvol1, mouse OVOL1 (GenBank acc. no. AF134804); hOvol1, human OVOL1 (GenBank acc. no. AF016045); mOvol2, mouse OVOL2 (GenBank acc. no.AY090537); hOvol2, human OVOL2 (GenBank acc. no. AK022284); mOvol3, mouse OVOL3 (GenBank acc. no. BF714064); hOvol3, human OVOL3 (GenBank acc. no. AD001527).

The Ovo gene family encodes evolutionarily conserved proteins contain four DNA-binding C2H2 zinc fingers at the C termini and possess transcriptional regulatory activities in diverse array of organisms from Caenorhabditis elegansDrosophilaZebrafish, chick, and mammals.  Drosophila ovo, the founding member of the family, acts genetically downstream of Wg (fly Wnt homolog) and DER (fly epidermal growth factor receptor homolog) signaling pathways and is required for epidermal denticle formation and oogenesis.

OVOL proteins are characterized by the presence of hypervariable ID regions.

A. Mouse OVOL1 has ID residues in the first 100 amino acids. B. Mouse OVOL2 possesses ID residues in the first 50 amino acids with a glycine-rich and serine rich region as marked in red color. C. Mouse OVOL3 has ID segments within the N-terminal 100 residues. DDrosophila OVO is intrinsically disordered with large patches of residue biasness as indicated by the red color. We used DISOPRED2 software [47] for the prediction of ID regions. The horizontal line indicates the ordered/disordered threshold for the default false positive rate of 5%. The ‘filter’ curve represents the outputs from DISOPRED2 and the ‘output’ curve represents the outputs from a linear support vector machine (SVM) classifier (DISOPREDsvm). The outputs from DISOPREDsvm are included to indicate shorter as low confidence predictions of disorder.

doi:10.1371/journal.pone.0039399.g001, http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039399)

This gene family is identified as mammalian Ovol (Ovo-like) genes, including Ovol1(movo1), Ovol2 (movo2), and Ovol3 (movo3) in mice and OVOL1OVOL2, andOVOL3 in humans. Ovol1 is the most studied compared to Ovol2 and Ovol3.

Kumar A, Bhandari A, Sinha R, Sardar P, et al. (2012) Molecular Phylogeny of OVOL Genes Illustrates a Conserved C2H2 Zinc Finger Domain Coupled by Hypervariable Unstructured Regions. PLoS ONE 7(6): e39399. doi:10.1371/journal.pone.0039399


Phylogenetic history of OVOL proteins using the Bayesian method. A. Full-length OVOL proteins. B. Selected region of OVOL proteins.

Posterior probabilities scores are depicted by various color balls. The placozoan OVOL protein (e_gw1.4.509.1) was used as the outgroup in this phylogenetic tree. Red x indicates sequence position, which did not accord with species phylogeny. BFL: B. floridae (lancelet), SPU: S. purpuratus (sea urchin), NVE: N. vectensis (sea anemone), HRO: H. robusta (annelids), LGI: L. gigantean (molluscs) and TAD: T. adhaerens(placozoan). Trees in figures 7A and 7B are generated using the MrBayes 3.2 [53] from alignments supplied in supplementary Files S1 and S2, respectively. (Figure 7 of doi:10.1371/journal.pone.0039399.g007, http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039399)

Fine scale analysis of gene expression in Drosophila melanogaster gonads reveals Programmed cell death 4 promotes the differentiation of female germline stem cells” Amy C Cash and Justen Andrews* BMC Developmental Biology 2012, 12:4 doi:10.1186/1471-213X-12-4 

”Regulatory and functional interactions between ovarian tumor and ovo during Drosophila oogenesis. “ Shannon Hinson, Janette Pettus, Rod N Nagoshi Mechanisms of Development Volume 88, Issue 1, 1 October 1999, Pages 3–14  http://www.sciencedirect.com/science/article/pii/S0925477399001677

Molecular phylogeny of OVOL genes illustrates a conserved C2H2 zinc finger domain coupled by hypervariable unstructured regions.” Kumar ABhandari ASinha RSardar PSushma MGoyal PGoswami CGrapputo A. PLoS One. 2012;7(6):e39399. doi: 10.1371/journal.pone.0039399. Epub 2012 Jun 21.

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.” Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ.

Nucleic Acids Res. 1997 Sep 1; 25(17):3389-402.




Chromosomal localization of OVOL1 gene from selected vertebrates, flanked by a set of conserved marker genes.   SIPA1: signal-induced proliferation-associated 1; RELA: v-rel reticuloendotheliosis viral oncogene homolog A (avian); KAT5: K (lysine) acetyltransferase; SNX32: sorting nexin 32; MUS81: MUS81 endonuclease homolog (S. cerevisiae); BANF1: barrier to autointegration factor 1; EXOC6B: exocyst complex component 6B; DYSF: dysferlin, limb girdle muscular dystrophy 2B; COL4A5: collagen, type IV, alpha 5; DAK: dihydroxyacetone kinase 2 S. cerevisiae homolog.   doi:10.1371/journal.pone.0039399.g003, http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039399)


Drosophila ovo/svb (dovo) is required for epidermal cuticle/denticle differentiation and is genetically downstream of the wg signaling pathway, so does a mouse homolog of dovomovo1.  Also, Li group showed that movo1 promoter is activated by the lymphoid enhancer factor 1 (LEF1)/β-catenin complex, a transducer of wnt signaling. Simply these data showed movo1 is a developmental target of wnt signaling during hair morphogenesis in mice, and there is a conserved regulatory pathway at wg/wnt-ovolink in epidermal appendage. human OVOL1 has been identified as a gene that is responsive to TGF-β1/BMP7 treatment via a Smad4-dependent pathway (Kowanetz et al., 2004).

Ovo1 li“Characterization of a human homolog (OVOL1) of the Drosophila ovo gene, which maps to chromosome 11q13.” Chidambaram A, Allikmets R, Chandrasekarappa S, Guru SC, Modi W, Gerrard B, Dean M. Mamm Genome. 1997 Dec;8(12):950-1.nks Wnt signaling with N-cadherin localization during neural crest migrationDevelopment 2010 137 (12) 1981-1990.

“Id2 and Id3 define the potency of cell proliferation and differentiation responses to transforming growth factor beta and bone morphogenetic protein.” Marcin Kowanetz

Ulrich ValcourtRosita Bergström,Carl-Henrik Heldin and Aristidis Moustakas*

. Mol. Cell. Biol., 24 (2004), pp. 4241–4254 http://mcb.asm.org/content/24/10/4241

“The LEF1/β-catenin complex activates movo1, a mouse homolog of Drosophila ovo required for epidermal appendage differentiation” Baoan LiDouglas R. MackayQian DaiTony W. H. LiMahalakshmi NairMagid Fallahi, Christopher P. SchonbaumJudith FantesAnthony P. MahowaldMarian L. Waterman,Elaine Fuchs, and Xing DaiPNAS  vol. 99 no. 9  Baoan Li,  6064–6069. http://www.pnas.org/content/99/9/6064.abstract?ijkey=a7d2985635ef09ca63982ae4397ef325aa46252b&keytype2=tf_ipsecsha


“Expression of murine novel zinc finger proteins highly homologous to Drosophila ovo gene product in testis.” Masu Y, Ikeda S, Okuda-Ashitaka E, Sato E, Ito S. FEBS Lett. 1998 Jan 16;421(3):224-8.

The ovo gene required for cuticle formation and oogenesis in flies is involved in hair formation and spermatogenesis in mice” Xing Dai, Christopher Schonbaum, Linda Degenstein, Wenyu Bai,Anthony Mahowald, and Elaine Fuchs. (1998) Genes Dev. 12, 3452–3463 http://www.ncbi.nlm.nih.gov/pubmed/9808631


OvoL2 at the Junction of Decisions:


Brain development is fascinating and complex since cranial neurulation is an integral component of brain morphogenesis  and there are factors present outside of the neuroepithelium can also affect the morphogenesis of the cranial neural tube.  Previous studies revealed Ovol2 expression in brain, testis, and epithelial tissues such as skin and intestine of adult mice (Li et al., 2002a).



OVOL2 orthologs identified in vertebrates by comparing chromosomal localization.

RRBP1: ribosome binding protein 1 homolog; BANF2: barrier to autointegration factor 2; SNX5: sorting nexin 5; CSRP2BP: CSRP2 binding protein; SEC23B: protein transport protein Sec23B; POLR3F: polymerase (RNA) III (DNA directed) polypeptide F; RBBP9: Retinoblastoma-binding  protein 9; DTD1: D-tyrosyl-tRNA deacylase 1. doi:10.1371/journal.pone.0039399.g004, http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039399)


Neural/non-neural cell fate decisions is carried by bone morphogenetic protein (BMP) signaling, which inhibits precocious neural differentiation and allows for proper differentiation of mesoderm, endoderm, and epidermis, during early embryonic development. There are many unknown in this mechanism yet the expression of Ovol2, which encodes an evolutionarily conserved zinc finger transcription factor, is down-regulated during neural differentiation of mouse embryonic stem cells since null Ovol2 in embryonic stem cells facilitates neural conversion and inhibits mesendodermal differentiation, whereas Ovol2 overexpression gives rise to the opposite phenotype. Furthermore, the studies also prove BMP4 and ovo2 interacted to rescue these changes. If BMP4 is provided,  Ovol2 knockdown partially rescues the neural inhibition.  Mechanism studies show the regulation pattern between these BMP and Ovol2.  BMP4 directly regulates Ovol2 expression through the binding of Smad1/5/8 to the second intron of the Ovol2 gene. Thus, Ovol2 acts downstream of BMP pathway.  In addition, in vivo chick studies presented that when Ovol2 is ectopically expressed the prospective neural plate represses the expression of the definitive neural plate marker cSox2In the chick embryo.  Also, lack of Ovol2 prevented increase BMP4 expression.  During early germ layer development there is an important comment between neuroectoderm and mesendoderm provided by Ovol2.

In addition, Ovol2 acts in downstream of key developmental signaling pathways including Wg/Wnt and BMP/TGF-β.  Based on findings from chromatin immunoprecipitation, luciferase reporter, and functional rescue assays, Wells group demonstrated that Ovol2 directly represses two critical downstream targets, c-Mycand Notch1.  Hence, this action suppresses keratinocyte transient proliferation and terminal differentiation.  Like a twilight zone to choose when to proliferate and when to resist differentiation.


Ovol2, a Mammalian Homolog of Drosophila ovo: Gene Structure, Chromosomal Mapping, and Aberrant Expression in Blind-Sterile Mice.” Baoan Li, Qian Dai, Ling Li, Mahalakshmi Nair, Douglas R. Mackay, Xing DaiGenomics Volume 80, Issue 3, September 2002, Pages 319–325.

Ovol2 directly represses two critical downstream targets, c-Myc and Notch1, thereby suppressing keratinocyte transient proliferation and terminal differentiation, respectively

Wells JLee BCai AQKarapetyan ALee WJRugg ESinha SNie QDai X.

J Biol Chem. 2009 Oct 16;284(42):29125-35. doi: 10.1074/jbc.M109.008847. Epub 2009 Aug 21.

The zinc finger transcription factor Ovol2 acts downstream of the bone morphogenetic protein pathway to regulate the cell fate decision between neuroectoderm and mesendoderm.” Zhang T, Zhu Q, Xie Z, Chen Y, Qiao Y, Li L, Jing N. J Biol Chem. 2013 Mar 1;288(9):6166-77. doi: 10.1074/jbc.M112.418376. Epub 2013 Jan 14.

The mouse Ovol2 gene is required for cranial neural tube development”  Douglas R. MackayaMing Hua,   Baoan LiaCatherine RhéaumeaXing Dai.l Developmental Biology Volume 291, Issue 1, 1 March 2006, Pages 38–52. 


While tracing the OVOL genes, we identified a third OVOL gene, OVOL3, in a wide array of mammals including humans (chromosome 19), chimpanzees (chromosome 19), mice (chromosome 7), rats (chromosome 1), cows (chromosome 18), pigs (chromosome 6), and opossums (chromosome 4) with a conserved synteny. The conserved synteny comprises an octet of genes, LIN37-PRODH2-KIRREL2-APLP11-NKF3ID-LPFN3​-SDHAF1-CLIF3,on one side and POLR2L-CAPSN1-COX7A1 on the other side of OVOL3 in a region of about 400 kb (Figure 5 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039399).

Synteny analysis of OVOL3 genes illustrates the loss of OVOL3a after duplication event and maintenance of paralogous OVOL3b in fishes.

LIN37: lin-37 homolog (C. elegans); PRODH2: proline dehydrogenase (oxidase) 2; KIRREL2: kin of IRRE like 2 (Drosophila); APLP1: amyloid beta (A4) precursor-like protein 1; NFKBID: nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, delta; LRFN3: leucine rich repeat and fibronectin type III domain containing 3; SDHAF1: succinate dehydrogenase complex assembly factor 1; CLIP3: CAP-GLY domain containing linker protein 3; POLR2I: polymerase (RNA) II (DNA directed) polypeptide I, 14.5 kDa; CAPNS1: calpain, small subunit 1; COX7A1: cytochrome c oxidase subunit VIIa polypeptide 1 (muscle); DMPK: dystrophia myotonica-protein kinase; HLCS: holocarboxylase synthetase; AMOT: angiomotin; REXO2: REX2 RNA exonuclease 2 homolog (S. cerevisiae). (Reference from doi:10.1371/journal.pone.0039399.g005 , http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039399)

There are not many studies on Ovol 3but my interest in this region lies on Chromosome 19 since “it has the highest gene density of all human chromosomes and the large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance.”

The DNA sequence and biology of human chromosome 19.” Grimwood J, et al.  Nature. 2004 Apr 1;428(6982):529-35.

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John Rinn - Genomic Garbage Man

John Rinn – Genomic Garbage Man (Photo credit: ChimpLearnGood)

DNA: One man’s trash is another man’s treasure, but there is no JUNK after all

Author: Demet Sag, PhD

One man’s trash is another man’s treasure, but there is no JUNK after all:

The JUNK has a meaning


Long non-coding RNAs recognized after transcriptome sequencing and studied more closely recently thanks to genomic tiling arrays, cDNA sequencing and RNA-Seq, which they have provided initial insights into the extent and depth of transcribed sequence across human and other genomes. How many are there in the genome? What are their mechanisms? How can we use them in molecular diagnostics and targeted therapies?  How do they effect the function in a disease? Is it possible to modulate gene expression at the level of stem cell to redirect the cell differentiation? These are the main questions that we are looking for.

In early 90s actually first lincRNA was described, Xist. The main function was dosage compensation. Then in 2000s FANTOM consortium project changed the perspective on these long transcripts. Then they are called natural antisense transcripts (NATs), because very large number of these transcripts is overlapping with, and is transcribed in the antisense direction, to protein-coding genes.  As a result of this study 11000 lincRNA discovered from full length cDNAs in mice. Later, yet another shift occur since these transcribed units are solely located in the introns or within “junk” DNA of protein-coding genes.  Another independent study quantified that about 40% of protein-coding genes express NATs. Proven that there is nothing junk about DNA. Then, it was found that there are 8000 lincRNAs and among these 4000 are determined since they provide cell identity with multi-exogenic, polyadenylated, capped, ether in the cytoplasm or in the nucleus. However, even more recent studies show that there are about 20,000 lincRNAs.  Furthermore, lincRNAs are classified under three distinct class: 1. Long-non-coding RNAs away from protein-coding genes, 2 NATs transcribed from the opposite strand of protein-coding genes, 3. Intronic lincRNAs expressed from within the introns of protein coding genes.


English: The human genome, categorized by func...

The human genome, categorized by function of each gene product, given both as number of genes and as percentage of all genes. (Photo credit: Wikipedia)

Their function is under study. However, keep in mind that they are redundant, so deleting or creating null mutations may or may not answer specific development questions. On the other hand, epigenetics, gene imprinting, and pathologies can be the best resource to identify their specific roles in biological functions and interactions.  Distinct gene regulation either as a cis or trans element, gene imprinting, modulating alternative splicing, nuclear organization, determining a chromatin structure are under study.  This will allow us to relate genome structure and function in health and disease better.  Identification of their function during biological responses require a long way to be completed due to complexity since lincRNAs also regulate microRNAs.  Regardless of many obstacles there is a progress.  Disregulation of these lincRNA mainly observed in several cancer types, prostate, breast, hepatocellular carcinoma, colorectal, glioma and melanoma, possibly more. Most of the studies are done in vitro. However, there are many great model organism work as well, such as mice, zebra fish, and worm.

It was also not surprising that their regulation possibly under control of hormones based on circadian clock of our body. So better to sleep eight hour a day is not a cliché.


Next topic will include understanding of lincRNA mechanisms and epigenetics followed by lincRNAs during disease and cellular genesis.


Mechanism, Genome and Genetics:

Long non-coding RNAs: insights into functions. Mercer TR, Dinger ME, Mattick JS Nat. Rev. Genet. 2009;10:155159. http://www.ncbi.nlm.nih.gov/pubmed/19188922


Long Noncoding RNAs: Past, Present, and Future” Genetics 1 March 2013: 651-669. http://www.genetics.org/content/193/3/651.abstract


“RNA-protein analysis using a conditional CRISPR nuclease” Proc. Natl. Acad. Sci. USA 2 April 2013: 5416-5421. http://www.pnas.org/content/110/14/5416.abstract

“Noncoding RNA and Polycomb recruitment” RNA 1 April 2013: 429-442. http://rnajournal.cshlp.org/content/19/4/429.abstract


“Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs” Nucleic Acids Res 1 August 2012: 6391-6400. http://nar.oxfordjournals.org/content/40/14/6391.abstract



“Long noncoding RNAs regulate adipogenesis” Proc. Natl. Acad. Sci. USA 26 February 2013: 3387-3392. http://www.pnas.org/content/110/9/3387.abstract


“Circadian changes in long noncoding RNAs in the pineal gland” Proc. Natl. Acad. Sci. USA 14 August 2012: 13319-13324. http://www.pnas.org/content/109/33/13319.abstract

Animal and Development:

“Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis” Genome Res 1 March 2012: 577-591. http://genome.cshlp.org/content/22/3/577.abstract


“Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm” Genome Res 1 April 2011: 578-589. http://genome.cshlp.org/content/21/4/578.abstract

Long noncoding RNAs in C. elegans” Genome Res 1 December 2012: 2529-2540. http://genome.cshlp.org/content/22/12/2529.abstract

A spatial and temporal map of C. elegans gene expression” Genome Res 1 February 2011: 325-341. http://genome.cshlp.org/content/21/2/325.abstract


“SFMBT1 functions with LSD1 to regulate expression of canonical histone genes and chromatin-related factors” Genes Dev. 1 April 2013: 749-766. http://genesdev.cshlp.org/content/27/7/749.abstract

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Reporter: Aviva Lev-Ari, PhD, RN

The 6/13/2013 Supreme Court Decision is covered on this Open Access Online Scientific Journal

Genomics & Ethics: DNA Fragments are Products of Nature or Patentable Genes?

Geneticist Ricki Lewis, PhD: Genetics Errors in Supreme Court Decision of 6/13/2013

DNA Science BlogDNA Science Blog


Earlier today, my “in” box began to fill with info from everyone I’ve ever met letting me know that the Supreme Court had ruled on the Myriad case about patenting the breast cancer genes BRCA1 and BRCA2. I also received a dozen pitches from PR people offering me all manner of instant interviews with lawyers, doctors, bioethicists, and health care analysts.

No one offered me an interview with a geneticist – a person who knows something about DNA. So being such a person myself, I decided to take a look at the decision. And I found errors – starting right smack in the opening paragraph.

“Scientists can extract DNA from cells to isolate specific segments for study. They can also synthetically create exons-only strands of nucleotides known as composite DNA (cDNA). cDNA contains only the exons that occur in DNA, omitting the intervening exons.”

The definition is correct, the terminology, not. “cDNA” does not stand for “composite DNA.” It stands for “complementary DNA.”

cDNA came into fashion when I was in grad school, circa 1977. Like many genetics terms, it has a very precise meaning, something I pay attention to because I write human genetics books, including 10 editions of a textbook.

A cDNA is termed “complementary” because it is complementary in nucleotide base sequence to the messenger RNA (mRNA) that is made from the gene. Enzymes cut from the mRNA the sequences (introns) that do not encode amino acids and retains those (exons) that do encode protein. So a cDNA represents the part of a gene that is actually used to tell the cell to make protein. End of biology lesson.

A cDNA is created in the laboratory, and it is not a DNA sequence that occurs in nature. Hence, the Supreme Court’s part 2 of the decision, which acknowledges Myriad’s right to use a test based on a complementary, or cDNA.

I did a google search for “composite DNA” and just found the media parroting of today’s decision, and a few old forensics uses. So a caveat: my conclusion that the term is incorrect and invented is based on negative evidence. If I’m wrong, mea culpa in advance and I will feel like an idiot.

But cDNA isn’t the only error. I soon found another. On page 16, footnote #8 discusses a pseudogene as resulting from “random incorporation of fragments of cDNA.” That’s not even close to what a pseudogene is.

A pseudogene results from a DNA replication error that makes an extra copy of a gene. Over time, one copy mutates itself into a form that can’t do its job. The pseudogene remains in the genome like a ghost of a functional gene. The mutations occur at random because the pseudogene, not being used, isn’t subject to natural selection – that’s probably what the Court means by “random.” The globin gene locus on chromosome 11 is chock full of pseudogenes. This is such a classic example of basic genetics that my head is about to explode.

And how on earth is the Supreme Court’s definition of a pseudogene supposed to happen, in nature or otherwise? A cDNA exists in a lab dish. A gene exists in a cell that is part of an organism. How does the cDNA “randomly incorporate” itself inside the cell? Jump in from the dish? Part of the footnote states, “… given pseudogenes’ apparently random origins … ” Pseudogenes’ origins aren’t random at all. They happen in specific genes that tend to have repeats in the sequence, “confusing” the replication enzymes.

Today’s decision is undoubtedly a wonderful leap forward for patients, their families, and researchers. And some may think I am nitpicking. But these two errors jumped right out at me — I’d troll for more but I want to post this. What else is wrong? How can we trust the decision if the science is wrong? And what is the background of the people who research the decisions?

I know nothing about the law, zero, which is why I’m not writing about that. But the science in something as important as a Supreme Court decision should accurately use the language of the field under discussion.


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RNA Virus Genome as Bacterial Chromosome

Reporter: Larry H Bernstein, MD, FCAP


Engineering the largest RNA virus genome as an infectious bacterial artificial chromosome
F Almazan, JM Gonzalez, Z Penzes, A Izeta, E Calvo, J Plana-Duran, and L Enjuanes

PNAS  May 9, 2000; 97(10): 5516–5521.

the application of two strategies,

  • cloning of the cDNAs into a bacterial artificial chromosome and
  • nuclear expression of RNAs that are typically produced within the cytoplasm

is useful for the engineering of large RNA molecules.
A cDNA encoding an infectious coronavirus RNA genome

  • has been cloned as a bacterial artificial chromosome.

The rescued coronavirus

  • conserved all of the genetic markers introduced throughout the sequence and
  • showed a standard mRNA pattern and

the antigenic characteristics expected for the synthetic virus.
The cDNA was transcribed

  • within the nucleus, and
  • the RNA translocated to the cytoplasm.
Interestingly, the recovered virus had
  • essentially the same sequence as the original one, and
      • no splicing was observed.

During the engineering of the infectious cDNA,

  • the spike gene of the virus was replaced by
  • the spike gene of an enteric isolate.

The synthetic virus

  • replicated abundantly in the enteric tract and was fully virulent, demonstrating that
  • the tropism and virulence of the recovered coronavirus can be modified.

the application of two strategies,

  • cloning of the cDNAs into a bacterial artificial chromosome and
  • nuclear expression of RNAs that are typically produced within the cytoplasm,
    • is useful for the engineering of large RNA molecules.

A cDNA encoding an infectious coronavirus RNA genome has been cloned as a bacterial artificial chromosome. The rescued coronavirus

  • conserved all of the genetic markers introduced throughout the sequence and
  • showed a standard mRNA pattern and
  • the antigenic characteristics expected for the synthetic virus.
    • The cDNA was transcribed within the nucleus, and
    • the RNA translocated to the cytoplasm.

Interestingly, the recovered virus had essentially the same sequence as the original one, and no splicing was observed. During the engineering of the infectious cDNA, the spike gene of the virus was replaced by the spike gene of an enteric isolate. The synthetic virus

  • replicated abundantly in the enteric tract and
  • was fully virulent,

demonstrating that the tropism and virulence of the recovered coronavirus can be modified.}

Description: The interaction of mRNA in a cell...

Description: The interaction of mRNA in a cell. Source: http://www.genome.gov/Pages/Hyperion/DIR/VIP/Glossary/Illustration/mrna.shtml (file) License: “All of the illustrations in the Talking Glossary of Genetics are freely available and may be used without special permission.” http://www.genome.gov/page.cfm?pageID=10003803 (Photo credit: Wikipedia)

RNA Protein Virus

RNA Protein Virus (Photo credit: Wikipedia)

This image was created as part of the Philip G...

This image was created as part of the Philip Greenspun illustration project. (Photo credit: Wikipedia)

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Genomics and Ethics: DNA Fragments are Products of Nature or Patentable Genes?

Curator: Aviva Lev-Ari, PhD, RN


Experts say court’s decision on human gene patents is a win-win

Jun 16, 2013

Jun 16, 2013 (St. Louis Post-Dispatch – McClatchy-Tribune Information Services via COMTEX News Network) — The Supreme Court ruling Thursday that naturally occurring human genes cannot be patented effectively ended the monopoly that Utah-based Myriad Genetics had on breast and ovarian cancer tests.

The news was hailed as a victory by health advocates and medical researchers, who can now not only access the genes at issue — the BRCA1 and BRCA2 — but all other patented human genes without infringement. In the wake of the decision, several other testing companies, including Quest Diagnostics, announced it would perform the tests — and at far cheaper prices than Myriad’s.

The court’s unanimous ruling, however, was mixed. It said that naturally occurring DNA could not be patented, but synthetic DNA can still be, giving patent protection advocates and Myriad a victory, too. The decision also means that methods of isolating genes still qualify for patent protection.

The Post-Dispatch interviewed experts from a broad range of fields, from medicine to law, about the court’s ruling.

Here’s what they had to say about what was at stake and what the decision could mean.

Christopher Mason

Professor of physiology, biophysics and computational biomedicine, and author of a study showing that 41 percent of the human genome is covered by patents, Cornell University

I’d say this represents a great win for genetic liberty, both for patients and for doctors. The American Medical Association said it was a big win for patients, and I couldn’t agree more — especially for breast and ovarian cancer, but for all types of cancer. This is an important cancer gene and now it’s open for study to everyone.

(Myriad) didn’t just own a test or a method, they owned anyone’s DNA as soon as it was isolated. They didn’t say we patented a series of letters, they said we patent anything that remotely looks like that, which the court correctly said is not patentable.

It would have been great to have both the patents (on natural and synthetic DNA), but of the two this is the most restrictive one — 99.9 percent of testing is done on DNA not cDNA.

Plenty of companies aren’t scared anymore. This is going to open the floodgates on new research and ideas.

Dr. Julie Margenthaler

Associate professor of surgery and breast cancer specialist, Siteman Cancer Center

This ruling has important implications for physician scientists actively engaged in genetic research. We are on the brink of significant strides in our understanding of the genetic links to many diseases.

For those of us who care for cancer patients, personalized cancer care hinges on the ability to genetically examine the pathways that result in a normal cell becoming a malignant cell. Because some companies held patents to pieces of the genome involved when whole genome sequencing is performed, there was at least some concern over patent infringement. With this ruling, we can continue to move our research forward and benefit the lives of our current and future patients.

Michael Watson

Executive director, American College of Medical Genetics and Genomics (plaintiffs in the case), and former professor of pediatrics at Washington University

It has enormous implications for labs and the public, certainly for breast cancer and for many other cancers. Since the case was settled (Thursday), at least four labs have put the test online. Prices are about half of Myriad’s — $3,500 down to $2,000 overnight.

It’s a win-win for everybody. It used to be when you had the tests done by Myriad, you couldn’t get that test confirmed by anyone else. Now the public can confirm the test and get second opinions, and that has a lot of value for patients. And I think it’ll open up the research.

There are two aspects of this that still remain open. Because 4,000 to 5,000 genes have patents on them, many people signed licensing agreements to use the gene. One of the questions is about the contract they signed. They will probably be able to challenge their contract now.

Nathan Lakey President and CEO, Orion Genomics

I think the ruling is positive because it removes a cloud of uncertainty as to where the Supreme Court stood on patents relating to gene sequences. I appreciate the thoughtfulness that went into the ruling. Justice Thomas adds a section that talks about what the ruling did not address that’s interesting. He emphasizes that method patents, or patents covering gene sequences that apply knowledge of those sequences, are patentable. I think this is what the justices sought to do, to not limit science and to not limit innovation and improvements in patient care. I think they do a markedly good job laying out the framework by which the business of science needs to consider the issue going forward as we all seek to lower the cost of care and improve outcomes.

We’re thrilled because our patents have been crafted primarily as method patents that involve naturally occurring gene sequences, and at the same time we add on to that a novel method that was not known and is quite valuable. We have biomarkers that we believe will be able to predict the risk of an individual getting colon cancer in the future, not unlike the Myriad test, but this is for colon cancer. We feel that our path forward is actually more clear and more positive given the clear line that the Supreme Court drew around what is and what isn’t patentable.

Janet S. Hendrickson

Patent attorney, specializing in chemical, pharmaceutical and food science companies, Senniger Powers law firm

They split it down the middle, and it seems to be, when looking at the commentary, that most people agree with that. They didn’t preclude the patenting of everything related to DNA, just natural DNA.

There are so many considerations and it’s hard to know what ramifications there are going to be, and what might be the best policy. It does mean that for companies that have these claims on natural DNA in their portfolio, they need to make sure they have the other range of claims for the cDNA (synthetic DNA). For companies that have past patents, it’s going to figure into those claims for those natural DNA products.

So it’s hard to tell whether it has broader implications for other things, that when you take them out of their natural milieu we thought were patentable.

Kevin Emerson Collins Professor, Washington University School of Law and patent law expert

This is going to mean one thing for patent lawyers and another thing for biotech companies. For patent lawyers, we now have a new source of business. The court hasn’t given us precise guidelines that say exactly when in other situations do we pass from something being a product of nature to a patentable invention. That’s a new frontier that patent lawyers are going to have to advise companies on.

For biotech companies it’s going to mean they pay patent lawyers a little more. Although the Myriad Genetics ruling deals with DNA, it would seem from the language of the opinion that the ruling should also apply to nongenetic, naturally occurring materials, but exactly how is yet to be determined.

A historical example that predates the Myriad controversy is the debate over the patentability of insulin in the early 20th century. A very famous lower court opinion held that isolated and purified human insulin was patentable so long as it became isolated insulin with impurities removed and took on new commercial value. I bet that case might well come out differently under the Myriad Genetics ruling. The insulin question is moot; that patent has expired. Similarly there a number of other therapeutics which are components that nature already makes that are isolated in a way they can be used in medicine but not in their natural state. Those are the kinds of things we’re going to have to grapple with.

Josh Newby-Harpole Founder, Theresa Harpole Foundation for Metastatic Breast Cancer in Alton

We have a foundation we started this year in honor of my mom. She was diagnosed over seven years ago with stage zero breast cancer. They did genetic testing and found out she had the BRCA gene. In 2010 she got diagnosed with metastatic breast cancer after she had a lump in her neck and it had spread to her bones. I needed to get tested at that point. I had testing done in Chicago and found out that I had the BRCA gene. As a male I’m lucky she had a son and not a daughter. My mom has been on different courses of treatment, and I monitor my health as well as I can, because I have a higher risk for certain kinds of cancer such as prostate and skin cancer and a higher than 3 percent chance of breast cancer.

The cost was probably over $2,000 to have the test done, and I paid close to $1,000 for it. We’re very excited about the Supreme Court ruling. I think a lot of people are hesitant to get the test done because of the cost. It’s exciting because it means possibilities. More people are going to be motivated to do research in labs to try to find a cure. Maybe they can come up with better treatment options for women because some of them will find out they have the gene and they don’t have evidence of disease. It’s something that is really getting a lot of attention right now, and the population is maybe not as aware about things like BRCA and metastatic breast cancer.

Yvette Liebesman Assistant professor of law, St. Louis University

It’s very good for research and in fact it’s very good for health care in the sense that already today a competitor for Myriad said they would run the same test for thousands less. Already we’re seeing a good thing happening that more women are going to be able to be tested for this gene. Now we’re talking about more women being aware of their health risks. Now a company that wants to develop a drug isn’t going to have to go through Myriad to isolate this gene in order to test drugs for breast cancer.

If Myriad won this case it would be like saying while a tree is made by nature, if I find a way to pick the leaves off it, the leaf is my patented product. Myriad did win in one sense, that there is a form of DNA not found in nature that is patentable. This is very logical. I think that like with most things, the people who are doomsayers will say it’s not going to have as great of an impact. The idea that now this opens up the ability to develop treatments is going to be huge.

___ (c)2013 the St. Louis Post-Dispatch Visit the St. Louis Post-Dispatch at
www.stltoday.com Distributed by MCT Information Services

Georgina Gustin and Blythe Bernhard

Copyright (C) 2013, St. Louis Post-Dispatch

SOURCE: Comtex


UPDATED 6/13/2013, following the new Supreme Court Decision on 6/13/2013 to include it, below.

The Supreme Court ruled unanimously Thursday that human genes cannot be patented, a decision that could shape the future of medical and genetic research and have profound effects on pharmaceuticals and agriculture.The ruling was a split decision for Myriad Genetics Inc., which holds patents on genes that have been linked to breast and ovarian cancer.

Justice Clarence Thomas, writing for the court, said that merely isolating those specific genes — called BRCA1 and BRCA2 — was not worthy of a patent.

“Myriad found the location of the BRCA1 and BRCA2 genes, but that discovery, by itself, does not render the BRCA genes . . . patent eligible,” Thomas wrote.On the other hand, Thomas wrote, Myriad’s creation of a synthetic form of DNA — called cDNA — based on its discovery does deserve patent protection.“The lab technician creates something new when cDNA is made,” Thomas wrote.Responding to the decision, Myriad focused on the favorable cDNA ruling. “We believe the court appropriately upheld our claims on cDNA, and underscored the patent eligibility of our method claims, ensuring strong intellectual property protection for our BRACAnalysis test moving forward,” said Peter D. Meldrum, company president and chief executive. “More than 250,000 patients rely upon our BRACAnalysis test annually, and we remain focused on saving and improving peoples’ lives and lowering overall health-care costs.”DNA research is a vital component of personalized medicine. The challenge to Myriad’s patents came from scientists and doctors who said that allowing patents on genes inflated the cost of testing and hindered research.

The American Civil Liberties Union praised the high court’s ruling as a victory. “Today, the court struck down a major barrier to patient care and medical innovation,” said Sandra Park of the ACLU, which represented the groups that brought the challenge. “Because of this ruling, patients will have greater access to genetic testing, and scientists can engage in research on these genes without fear of being sued.”

The test that Myriad offers for determining whether a woman contains the genetic mutation that heightens her chance of cancer has received much attention lately after actress Angelina Jolie wrote about it in a letter to the editor to the New York Times. In the letter, Jolie revealed that she had a double mastectomy because the test showed she carried the defective gene.


[bold and green added by the Curator]


1 (Slip Opinion) OCTOBER TERM, 2012


NOTE: Where it is feasible, a syllabus (headnote) will be released, as is being done in connection with this case, at the time the opinion is issued.The syllabus constitutes no part of the opinion of the Court but has been prepared by the Reporter of Decisions for the convenience of the reader. See United States v. Detroit Timber & Lumber Co., 200 U. S. 321, 337.






No. 12–398. Argued April 15, 2013—Decided June 13, 2013

Each human gene is encoded as deoxyribonucleic acid (DNA), which takes the shape of a “double helix.” Each “cross-bar” in that helix consists of two chemically joined nucleotides. Sequences of DNA nucleotides contain the information necessary to create strings of amino acids used to build proteins in the body. The nucleotides that code for amino acids are “exons,” and those that do not are “introns.” Scientists can extract DNA from cells to isolate specific segments for study. They can also synthetically create exons-only strands of nucleotides known as composite DNA (cDNA). cDNA contains only the exons that occur in DNA, omitting the intervening introns. Respondent Myriad Genetics, Inc. (Myriad), obtained several patents after discovering the precise location and sequence of the BRCA1 and BRCA2 genes, mutations of which can dramatically increase the risk of breast and ovarian cancer. This knowledge allowed Myriad to determine the genes’ typical nucleotide sequence, which, in turn, enabled it to develop medical tests useful for detecting mutations in these genes in a particular patient to assess the patient’s cancer risk. If valid, Myriad’s patents would give it the exclusiveright to isolate an individual’s BRCA1 and BRCA2 genes, and would give Myriad the exclusive right to synthetically create BRCA cDNA. Petitioners filed suit, seeking a declaration that Myriad’s patents areinvalid under 35 U. S. C. §101. As relevant here, the District Court granted summary judgment to petitioners, concluding that Myriad’s claims were invalid because they covered products of nature. The Federal Circuit initially reversed, but on remand in light of Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566 U. S. ___, the Circuit found both isolated DNA and cDNA patent eligible. 2 ASSOCIATION FOR MOLECULAR PATHOLOGY v. MYRIAD GENETICS, INC. Syllabus

Held: A naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated, but cDNA is patent eligible because it is not naturally occurring. Pp. 10–18. 

(a) The Patent Act permits patents to be issued to “[w]hoever invents or discovers any new and useful . . . composition of matter,” §101, but “laws of nature, natural phenomena, and abstract ideas”“ ‘are basic tools of scientific and technological work’ ” that lie beyond the domain of patent protection, Mayo, supra, at ___. The rule against patents on naturally occurring things has limits, however. Patent protection strikes a delicate balance between creating “incentives that lead to creation, invention, and discovery” and “imped[ing] the flow of information that might permit, indeed spur, invention.” Id., at ___. This standard is used to determine whether Myriad’s patents claim a “new and useful . . . composition of matter,” §101, or claim naturally occurring phenomena. Pp. 10–11. 

(b) Myriad’s DNA claim falls within the law of nature exception.Myriad’s principal contribution was uncovering the precise location and genetic sequence of the BRCA1 and BRCA2 genes. Diamond v. Chakrabarty, 447 U. S. 303, is central to the patent-eligibility inquiry whether such action was new “with markedly different characteristics from any found in nature,” id., at 310. Myriad did not create or alter either the genetic information encoded in the BCRA1 and BCRA2 genes or the genetic structure of the DNA. It found an important and useful gene, but ground breaking, innovative, or even brilliant discovery does not by itself satisfy the §101 inquiry. See Funk Brothers Seed Co. v. Kalo Inoculant Co., 333 U. S. 127. Finding the location of the BRCA1 and BRCA2 genes does not render the genes patent eligible “new . . . composition[s] of matter,” §101. Myriad’s patent descriptions highlight the problem with its claims: They detail the extensive process of discovery, but extensive effort alone isinsufficient to satisfy §101’s demands. Myriad’s claims are not saved by the fact that isolating DNA from the human genome severs the chemical bonds that bind gene molecules together. The claims are not expressed in terms of chemical composition, nor do they rely on the chemical changes resulting from the isolation of a particular DNA section. Instead, they focus on the genetic information encoded in the BRCA1 and BRCA2 genes. Finally, Myriad argues that the Patent and Trademark Office’s past practice of awarding gene patents is entitled to deference, citing J. E. M. Ag Supply, Inc. v. Pioneer Hi-Bred Int’l, Inc., 534 U. S. 124, a case where Congress had endorsed a PTO practice in subsequent legislation. There has been no such endorsement here, and the United States argued in the Federal Circuit and in this Court that isolated DNA was not patent eligible under §101. Pp. 12–16. 

3 Cite as: 569 U. S. ____ (2013)


(c) cDNA is not a “product of nature,” so it is patent eligible under§101. cDNA does not present the same obstacles to patentability as naturally occurring, isolated DNA segments. Its creation results in an exons-only molecule, which is not naturally occurring. Its order of the exons may be dictated by nature, but the lab technician unquestionably creates something new when introns are removed from a DNA sequence to make cDNA. Pp. 16–17.

(d) This case, it is important to note, does not involve method claims, patents on new applications of knowledge about the BRCA1 and BRCA2 genes, or the patentability of DNA in which the order of the naturally occurring nucleotides has been altered. Pp. 17–18. 

689 F. 3d 1303, affirmed in part and reversed in part. 

THOMAS, J., delivered the opinion of the Court, in which ROBERTS,  C. J., and KENNEDY, GINSBURG, BREYER, ALITO, SOTOMAYOR, and KAGAN, JJ., joined, and in which SCALIA, J., joined in part. SCALIA, J., filed an opinion concurring in part and concurring in the judgment.

1 Cite as: 569 U. S. ____ (2013) Opinion of SCALIA, J.


No. 12–398



[June 13, 2013]

JUSTICE SCALIA, concurring in part and concurring in the judgment. 

I join the judgment of the Court, and all of its opinion except Part I–A and some portions of the rest of the opinion going into fine details of molecular biology. I am un-able to affirm those details on my own knowledge or even my own belief. It suffices for me to affirm, having studied the opinions below and the expert briefs presented here, that the portion of DNA isolated from its natural state sought to be patented is identical to that portion of the DNA in its natural state; and that complementary DNA (cDNA) is a synthetic creation not normally present in nature.




Evolution of the case ASSOCIATION FOR MOLECULAR PATHOLOGY ET AL. v. MYRIAD GENETICS, INC., ET AL. priot to 6/13/2013 Supreme Court decision

Curator: Aviva Lev-Ari, PhD, RN

In an amicus brief, the Broad Institute‘s Eric Lander shares his personal view of the ongoing gene patenting case between Myriad Genetics and the American Civil Liberties Union, saying that isolated DNA fragments are products of Nature.

The central issue of the case revolves around Myriad’s patents on the BRCA1 and BRCA2 genes. In a mixed ruling, the federal appeals court found that while some of the company’s methods patents may not be patentable, its BRCA1 and BRCA2 gene patents, as they concern isolated DNA fragments, are patentable items as human intervention is needed to isolate DNA.

Lander argues that that is not true, though, as the Boston Globe points out, his brief was not filed in support of either side. Isolated DNA, he says, happens all the time in nature. “It is well-accepted in the scientific community that

(a) chromosomes are constantly being broken into DNA fragments by natural biological processes that break the covalent bonds within DNA chains;

(b) these DNA fragments can be routinely found in the human body … and

(c) these fragments cover the entire human genome and, in particular, include many of the DNA fragments claimed by Myriad’s patents,” the brief says.

The US Supreme Court announced in December that it will re-hear the Myriad gene patenting case.


Eric Lander weighs in on gene patenting case

By Carolyn Y. Johnson


FEBRUARY 26, 2013

Late last year, the nation’s highest court said it would consider a legal challenge to patents that biotechnology company Myriad Genetics holds on breast cancer genes. Now, Eric Lander, head of the Broad Institute in Cambridge, has filed an amicus brief that he says reflects his personal opinion. Utah-based Myriad, Lander argues, has patented products of nature, and its patents are an “insurmountable barrier” to studying DNA, with serious repercussions for medical progress.
In the Supreme Court of the United States – On Writ of Certiorari to the United States Court of Appeals for the Federal Circuit
The Association for Molecular Pathology, et al., v. Mariad Genetics, Inc, et al.,
Brief for Amicus Curiae Eric S. Lander in support of neither party
Eric S. Lander et al., Initial Sequencing and Analysis of the Human Genome, 409 Nature 860 (2001)
Eric S. Lander, Initial Impact of the Sequencing of the Human Genome, 470 Nature 187 (2011)
It is well-accepted in the scientific community that isolated DNA fragments of the human genome – including isolated DNA fragments of the BRCA1 and BRCA2 genes – are found routinely in th human body and are thus patent-ineligible products of Nature. The biotechnology industry would not be substantially affected by a narrowly crafted decision here holding that
1) fragments of human genome DNA are patent-ineligible where the claimed molecules themselves are routinely found in Nature and where the process for purification or synthesis of such molecules iS routine and
(2) cDNAs are patent-eligible.

Susan McBee and Bryan Jones Guest

Posted Thu, February 7th, 2013 10:16 am

The Supreme Court should be mindful of naturally derived products other than nucleic acids when deciding Myriad

The following contribution to our gene patenting symposium come from Susan McBee and Bryan Jones. Ms. McBee is the Chair of the Life Sciences Intellectual Property Team for Baker, Donelson, Bearman, Caldwell, and Berkowitz, P.C. Bryan Jones is a registered patent attorney in the Washington D.C. office of Baker, Donelson, Bearman, Caldwell, and Berkowitz, P.C.  

In April, the Supreme Court will hear oral argument in Association for Molecular Pathology v. Myriad, ostensibly on the question whether so-called “gene patents” satisfy 35 U.S.C. § 101.  However, Myriad is about more than whether “genes” can be patented.  It is about what types of activities justify patent protection.  Does one need to create something that is unlike anything else that has ever existed in order to justify a patent?  Or is it enough to discover something that was previously unknown, remove it from its natural environment, and show that it has a practical application?

This is a critical question to the biotechnology industry, because many biotechnological products are not novel chemical structures, but naturally occurring products.  Between 1981 and 2006, approximately forty percent of all pharmaceuticals approved for use by the FDA were a biologic, natural product, or derived from a natural product.  Moreover, for start-up biotechnology companies, patents covering such products are incredibly important, “as they are often the most crucial asset they own in a sector that is extremely research-intensive and with low imitation costs.” Strong and enforceable patents to these core products therefore are vitally important to the healthy development of the biotechnology industry.

Before the Myriad case, the Court has not had an opportunity to consider the patentability of such products.  Therefore, this case has the potential to have an enormous impact on the viability of the business model in this industry.

In Myriad, Judge Lourie and Judge Moore both found “isolated” nucleic acids to be patentable, but for different reasons.  Judge Lourie was convinced that isolated nucleic acids are patentable because isolation “breaks covalent bonds” relative to the longer native nucleic acid, thereby resulting in a new chemical entity.  Judge Moore reasoned that, if analyzed on a blank slate, she would require the product to have a “substantial new utility” relative to its natural function in order to satisfy 35 U.S.C. § 101.  While we agree that the generation of a novel chemical entity or demonstration of a new utility would be sufficient to satisfy 35 U.S.C. § 101, we do not believe these to be necessary requirements.

Consider, for example, Taq polymerase.  The inclusion of Taq into a process called polymerase chain reaction (PCR) has often been credited as being the single most important technological advance to the modern biotechnology industry.  PCR uses repeated cycles of increasing and decreasing temperatures in the presence of a polymerase to amplify a target nucleic acid.  In the original iteration of PCR, new polymerase enzyme had to be added to the reaction mixture after each heat cycle, because the high temperature permanently deactivated the enzyme.  Taq, however, is heat stable and thus does not lose activity when subjected to high temperatures.  Because of this stability, Taq only needs to be added to a PCR reaction mixture once, thus greatly reducing the costs and the time of performing the process, and permitting easy automation.  Clearly, then, the identification and characterization of this enzyme is a significant technological advance, from which the public obtains a significant benefit.  Yet the properties of Taq that make it so attractive for PCR are a consequence of its structure and function in the natural world.  Taq is naturally produced by Thermus aquaticus, a bacterium that is naturally found in hot springs.  Therefore, in nature, just like in PCR, Taq functions as a thermostable enzyme that catalyzes the amplification of a nucleic acid.  Why should this render Taq unpatentable?

The Constitution does not require a claimed compound to have a formally “new” chemical structure or new function to justify a patent.  Article I, section 8 of the Constitution authorizes patents “[t]o promote the Progress of Science and useful Arts . . . .”  As explained by the Court:

Congress may not authorize the issuance of patents whose effects are to remove existent knowledge from the public domain, or to restrict free access to materials already available.  Innovation, advancement, and things which add to the sum of useful knowledge are inherent requisites in a patent system which by constitutional command must ‘promote the Progress of useful Arts.’  This is the standard expressed in the Constitution and it may not be ignored.

Thus, the Constitution only limits patents that “remove existent knowledge from the public domain” or “restrict free access to materials already available.”  Assuming that Taq was not previously known, a claim to it in isolated form simply cannot “remove existent knowledge from the public domain.”  Because Taq naturally exists only in the context of a living organism, claiming it in “isolated” form cannot “restrict free access to” its source.  Thus, constitutional limits cannot justify a prohibition on patents covering isolated naturally occurring products.

Nor does 35 U.S.C. § 101 clearly prohibit such patents.  The statute specifically encompasses “discoveries,” so long as those discoveries relate to processes, compositions of matter, or articles of manufacture that are “new” and “useful.”  In most cases, naturally occurring products are found in very minute quantities in complex association with other molecules inside living organisms.  The act of isolating the natural product removes them from this context, thereby inevitably resulting in a composition that is materially different than anything that exists in nature.  An “isolated” natural product therefore is “new” compared to the same product in its natural state.  Its discovery thus could justify a claim under 35 U.S.C. § 101.

Finally, Supreme Court precedent does not clearly prohibit patenting of such claims.  Under the closest Supreme Court precedent, a patent that is limited to a “non-naturally occurring article of manufacture or composition of matter” satisfies 35 U.S.C. § 101.  Although it is often convenient to describe naturally occurring compounds in terms of chemical structure or nucleotide or amino acid sequence, they rarely if ever exist in nature as isolated compositions.  Rather, they are found in complex associations with other compositions, usually within living organisms.  The removal of these products from their natural context sometimes results in distinct chemical entities, such as the isolated nucleic acids in Myriad.  Other times, the result is a highly purified form of the compound, such as isolated adrenaline or purified vitamin B12.  In each case, however, the intervention of man is required to produce the “isolated” composition.  Claims directed to “isolated” natural compounds thus are limited to purely artificial, non-naturally occurring compositions of matter.  This should make them patentable, irrespective of whether they have a novel chemical structure or new utility in isolated form.

It is our sincere hope that the Court will not only find isolated nucleic acids to be patentable, but that it will do so under a rationale which allows for other naturally derived products to similarly be patentable.  In as much as a possible test can be garnered, our recommendation is to find that a naturally derived product satisfies 35 U.S.C. § 101 as long as it is claimed in a purely man-made form (and thus is “new”), and the form in which it is claimed has a practical utility disclosed in the Specification (and thus is “useful”).  This test closely aligns with the plain language of 35 U.S.C. § 101.  Challenges to the eligibility of such claims could then focus on two clear issues: (1) whether the claim encompasses the product in its natural state; and (2) whether the claim is reasonably commensurate in scope with the disclosed utility (i.e., is the claim narrowly tailored to products that possess the disclosed utility?).  This allows overly broad claims to be invalidated without resorting to a categorical ban on a broad class of subject matter.  Moreover, it would not require courts to answer the philosophical question of whether something has enough of a structural or functional change to justify a patent.

Posted in Association for Molecular Pathology v. Myriad GeneticsFeaturedGene Patenting Symposium

Recommended Citation: Susan McBee and Bryan Jones, The Supreme Court should be mindful of naturally derived products other than nucleic acids when deciding Myriad, SCOTUSblog (Feb. 7, 2013, 10:16 AM), http://www.scotusblog.com/2013/02/the-supreme-court-should-be-mindful-of-naturally-derived-products-other-than-nucleic-acids-when-deciding-myriad/

– See more at: http://www.scotusblog.com/?p=159001#sthash.UGzQgi2x.dpuf

Appeals Court Affirms Isolated DNA Patents in Myriad Case

August 16, 2012

NEW YORK (GenomeWeb News) – A federal appeals court today has for a second time reversed a lower district court’s decision that isolated genes are not patentable, but it also partly affirmed the District Court’s decision that certain methods patents “comparing” or “analyzing” gene sequences may not be patentable.

The Supreme Court recently asked the US Court of Appeals for the Federal Circuit to reconsider its earlier decision in the case, The Association for Molecular Pathology v. the US Patent and Trademark Office and Myriad Genetics, in light of its ruling in another lawsuit, called Mayo Collaborative Services v. Prometheus Laboratories.

AMP v USPTO focuses on the patentability of Myriad Genetics’ claims on isolated gene sequences and diagnostic methods related to its BRACAnalysis test. In Mayo v Prometheus, the Supreme Court recently invalidated patents held by diagnostics firm Prometheus because they merely described laws of nature, and did not apply those laws of nature in a markedly different manner as to warrant a patent.

Despite the Supreme Court’s ruling in Mayo, the CAFC in a 2-1 decision maintained that although isolated gene sequences may be derived from naturally occurring substances, their isolation requires human intervention in order to make them useful in medical care and so are deserving of patent protection.

“We are very pleased with the favorable decision the Court rendered today which again confirmed that isolated DNA is patentable,” Myriad Genetics President and CEO Peter Meldrum said in a statement. “Importantly, the court agreed with Myriad that isolated DNA is a new chemical matter with important utilities which can only exist as the product of human ingenuity.”

The decision was met with disappointment by those opposing gene patenting.

“It is extremely disappointing that despite the Supreme Court’s ruling, the appeals court has failed to fully re-consider the facts of this case,” Chris Hansen, a staff attorney with the ACLU Speech, Privacy and Technology Project, said in a statement.

The case against Myriad was filed in 2009 by the Public Patent Foundation, American Civil Liberties Union, AMP, and others who claim that patents cannot cover natural phenomena and that Myriad’s patents, and others like them, will hinder genetics research and keep some people from accessing tests and second opinions.

“This ruling prevents doctors and scientists from exchanging their ideas and research freely,” Hansen added the ACLU statement today. “Human DNA is a natural entity like air or water. It does not belong to any one company.”

Myriad said again today what it has argued all along, that gene patents have not thwarted research, that the cost of its BRACAnalysis test is not prohibitive and is covered through most insurance for “appropriate” patients, and that second opinion testing is available in many US labs.

“Certainly, you could hear a collective sigh of relief from the biotech industry, as of this decision,” Jennifer Camacho, an attorney and shareholder with law firm Greenberg Traurig, told GenomeWeb Daily News today.

“Isolated DNA patents remain intact. We still have patent eligibility for isolated DNA,” Camacho said, explaining that the court’s decision to uphold the patentability of isolated DNA may be seen by the biotech industry as more important than its reading of the reach of the Prometheus decision.

“They did actually take [the Prometheus decision] into consideration,” Camacho said, adding that it did not change the judges’ analysis.

“This puts a narrow interpretation of Prometheus in the books, as being limited to the ‘laws of nature’ exclusion, she added.

Camacho told GWDN that she was struck by how similar today’s CAFC ruling was to the original. She pointed out that part of one judge’s opinion, which argued that whether some patents should or should not be awarded are policy questions that are best left to Congress, was the same language as in the first opinion.

For Myriad, the ruling provided mixed results, Goldman Sachs Investment Research analyst Isaac Ro said in a note today.

On the positive side for Myriad, the patent eligibility of its BRCA1 and BRCA2-based tests was upheld again based on its isolated DNA claims and screening method claims. But a potential negative is that the CAFC also upheld the District Court’s opinion that Myriad’s method claims for comparing DNA sequences are not eligible.

“The outcome is modestly disappointing,” Ro stated, adding that the critical question now is whether or not the Supreme Court will agree to hear the case next year.

US Supreme Court Agrees to Hear Myriad Patent Case Again

NEW YORK (GenomeWeb News) – The US Supreme Court decided on Friday to once again hear the American Civil Liberty Union’s case against Myriad Genetics challenging the firm’s patent rights related to BRCA1 and BRCA2 genes.

The decision by the court to hear the case — originally filed by ACLU, the Public Patent Foundation, the Association for Molecular Pathology and others in 2009 — comes a little more than three months after a federal appeals courtissued a mixed ruling in which it found that isolated genes are patentable, but that certain methods patents that compare or analyze gene sequences may not be.

The US Court of Appeals for the Federal Circuit issued its decision in August after the Supreme Court asked it in March to reconsider a decision rendered by the appeals court in 2011 in light of the Supreme Court’s decision in another case, Mayo Collaborative Services v. Prometheus Laboratories. In that case, the Supreme Courtinvalidated patents held by Prometheus, saying the patents merely described laws of nature but did not apply those laws of nature in a markedly different manner as to warrant a patent.

The appeals court originally ruled in July 2011 that Myriad’s patents covering isolated DNA are patentable under Section 101 of the US Patent Act, reversing a decision by the Federal District Court for the Southern District of New York that isolated DNA is not much different from gene sequences found in nature and therefore is not patentable.

This past September, ACLU and the Public Patent Foundation asked the Supreme Court to once again take up the issue of whether Myriad’s claims on genes that predict the risk of ovarian and breast cancer can be patented. ACLU and the foundation contend that Myriad’s BRCA1 and BRCA2 gene patents should be invalidated because the genes are products of nature and allowing Myriad patent protection stifles scientific research and patient access to medical care.

“Myriad did not invent human genes, and has no right to claim ownership of them just because they removed them from the body,” Daniel Ravicher, executive director of PUBPAT, said in a statement on Friday. “The government does not have the right to give a corporation the exclusive power to control what we know about our own genetic makeup.”

Myriad President and CEO Peter Meldrum said in a statement, however, that patent protection is necessary to drive technological innovation.

“Two previous decisions by the Federal Circuit Court of Appeals confirmed the patentability of our groundbreaking diagnostic test that has helped close to 1 million people learn about their hereditary cancer risk,” he said. “Myriad devoted more than 17 years and $500 million to develop its BRACAnalysis test. The discovery and development of pioneering diagnostics and therapeutics require a huge investment and our US patent system is the engine that drives this innovation.

“This case has great importance for the hundreds of millions of patients whose lives are saved and enhanced by the life science industry’s products,” he said.

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