Feeds:
Posts
Comments

Posts Tagged ‘whole-genome sequences’

Exome Aggregation Consortium (ExAC), generated the largest catalogue so far of variation in human protein-coding regions: Sequence data of 60,000 people, NOW is a publicly accessible database

Posted in Exosomes, Population genetics, Variation in human protein-coding regions, tagged on August 18, 2016| Leave a Comment »

Exome Aggregation Consortium (ExAC), generated the largest catalogue so far of variation in human protein-coding regions: Sequence data of 60,000 people, NOW is a publicly accessible database

Reporter: Aviva Lev-Ari, PhD, RN

 

UPDATED on 8/22/2016

“The ExAC resource gives us incredible insight when evaluating a patient’s genome sequence in the clinic,” said Heidi Rehm, HMS associate professor of pathology at Brigham and Women’s Hospital, medical clinical director of the Broad’s Clinical Research Sequencing Platform and chief laboratory director of the Laboratory for Molecular Medicine at Partners HealthCare Personalized Medicine.

“In our own research, using the ExAC resource has allowed us to apply novel statistical methods to identify several new severe developmental disorders,” said Matthew Hurles, a researcher at the Wellcome Trust Sanger Institute and frequent user of the ExAC database. “Resources such as ExAC exemplify the benefits that can be achieved for families coping with rare genetic diseases, as a result of the mass altruism of many research participants who allow their data to be aggregated and shared.”

SOURCE

http://hms.harvard.edu/news/going-wide-and-deep?utm_source=Silverpop&utm_medium=email&utm_content=s3&utm_campaign=08.22.16.HMS

 

These variant data already guide diagnoses and treatment

E. V. Minikel et al. Sci. Transl. Med. 8, 322ra9; 2016

Quantifying prion disease penetrance using large population control cohorts

  1. Eric Vallabh Minikel1,2,3,4,*,
  2. Sonia M. Vallabh1,3,4,
  3. Monkol Lek1,2,
  4. Karol Estrada1,2,
  5. Kaitlin E. Samocha1,2,3,
  6. J. Fah Sathirapongsasuti5,
  7. Cory Y. McLean5,
  8. Joyce Y. Tung5,
  9. Linda P. C. Yu5,
  10. Pierluigi Gambetti6,
  11. Janis Blevins6,
  12. Shulin Zhang7,
  13. Yvonne Cohen6,
  14. Wei Chen6,
  15. Masahito Yamada8,
  16. Tsuyoshi Hamaguchi8,
  17. Nobuo Sanjo9,
  18. Hidehiro Mizusawa10,
  19. Yosikazu Nakamura11,
  20. Tetsuyuki Kitamoto12,
  21. Steven J. Collins13,
  22. Alison Boyd13,
  23. Robert G. Will14,
  24. Richard Knight14,
  25. Claudia Ponto15,
  26. Inga Zerr15,
  27. Theo F. J. Kraus16,
  28. Sabina Eigenbrod16,
  29. Armin Giese16,
  30. Miguel Calero17,
  31. Jesús de Pedro-Cuesta17,
  32. Stéphane Haïk18,19,
  33. Jean-Louis Laplanche20,
  34. Elodie Bouaziz-Amar20,
  35. Jean-Philippe Brandel18,19,
  36. Sabina Capellari21,22,
  37. Piero Parchi21,22,
  38. Anna Poleggi23,
  39. Anna Ladogana23,
  40. Anne H. O’Donnell-Luria1,2,24,
  41. Konrad J. Karczewski1,2,
  42. Jamie L. Marshall1,2,
  43. Michael Boehnke25,
  44. Markku Laakso26,
  45. Karen L. Mohlke27,
  46. Anna Kähler28,
  47. Kimberly Chambert29,
  48. Steven McCarroll29,
  49. Patrick F. Sullivan27,28,
  50. Christina M. Hultman28,
  51. Shaun M. Purcell30,
  52. Pamela Sklar30,
  53. Sven J. van der Lee31,
  54. Annemieke Rozemuller32,
  55. Casper Jansen32,
  56. Albert Hofman31,
  57. Robert Kraaij33,
  58. Jeroen G. J. van Rooij33,
  59. M. Arfan Ikram31,
  60. André G. Uitterlinden31,33,
  61. Cornelia M. van Duijn31,
  62. Exome Aggregation Consortium (ExAC)†,
  63. Mark J. Daly1,2 and
  64. Daniel G. MacArthur1,2,*

+ Author Affiliations

  1. ↵*Corresponding author. E-mail: eminikel@broadinstitute.org (E.V.M.); macarthur@atgu.mgh.harvard.edu (D.G.M.)

  • ↵† A list of consortium members appears at the end of this paper.

Science Translational Medicine  20 Jan 2016:
Vol. 8, Issue 322, pp. 322ra9
DOI: 10.1126/scitranslmed.aad5169

and

R. Walsh et al. Genet. Med. http://dx.doi.org/10.1038/gim.2016.90; 2016).

Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples

Genetics in Medicine
(2016)
doi:10.1038/gim.2016.90
Published online
17 August 2016

The ExAC project plans to grow over the next year to include 120,000 exome and 20,000 whole-genome sequences. It relies on the willingness of large research consortia to cooperate, and highlights the huge value of sharing, aggregation and harmonization of genomic data. This is also true for patient variants — there is a need for databases that provide greater confidence in variant interpretation, such as the US National Center for Biotechnology Information’s ClinVar database.

SOURCE

Nature536,249(18 August 2016)doi:10.1038/536249a

Read Full Post »