publication . Other literature type . Preprint . 2019

Pooled-parent exome sequencing to prioritise de novo variants in genetic disease

Harriet Dashnow; Katrina M. Bell; Zornitza Stark; Tiong Y. Tan; Susan M. White; Alicia Oshlack;
Open Access
  • Published: 07 Apr 2019
  • Publisher: bioRxiv
Abstract
<jats:title>Abstract</jats:title><jats:p>In the clinical setting, exome sequencing has become standard-of-care in diagnosing rare genetic disorders, however many patients remain unsolved. Trio sequencing has been demonstrated to produce a higher diagnostic yield than singleton (proband-only) sequencing. Parental sequencing is especially useful when a disease is suspected to be caused by a <jats:italic>de novo</jats:italic> variant in the proband, because parental data provide a strong filter for the majority of variants that are shared by the proband and their parents. However the additional cost of sequencing the parents makes the trio strategy uneconomical for...
Funded by
NHMRC| Harnessing the power of genomics to understand disease
Project
  • Funder: National Health and Medical Research Council (NHMRC) (NHMRC)
  • Project Code: 1126157
  • Funding stream: Career Development Fellowships
44 references, page 1 of 3

1. Glessner JT, Bick AG, Ito K, Homsy J, Rodriguez-Murillo L, Fromer M, et al. Increased frequency

2. Zaidi S, Choi M, Wakimoto H, Ma L, Jiang J, Overton JD, et al. De novo mutations in histonemodifying genes in congenital heart disease. Nature. 2013;498:220-3.

3. Brown TL, Meloche TM. Exome sequencing a review of new strategies for rare genomic disease research. Genomics. 2016;108:109-14.

4. Roach JC, Glusman G, Smit AFA, Huff CD, Hubley R, Shannon PT, et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science. 2010;328:636-9.

5. Clark MM, Stark Z, Farnaes L, Tan TY, White SM, Dimmock D, et al. Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases. npj Genomic Medicine. 2018;3:16.

6. de Ligt J, Willemsen MH, van Bon BWM, Kleefstra T, Yntema HG, Kroes T, et al. Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability. http://dx.doi.org/101056/NEJMoa1206524 [Internet]. Massachusetts Medical Society; 2012; Available from: https://www.nejm.org/doi/full/10.1056/nejmoa1206524

7. Rauch A, Wieczorek D, Graf E, Wieland T, Endele S, Schwarzmayr T, et al. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet. 2012;380:1674-82.

8. Vissers LELM, de Ligt J, Gilissen C, Janssen I, Steehouwer M, de Vries P, et al. A de novo paradigm for mental retardation. Nat Genet. 2010;42:1109-12. [OpenAIRE]

9. O'Roak BJ, Deriziotis P, Lee C, Vives L, Schwartz JJ, Girirajan S, et al. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet. 2011;43:585-9.

10. Veltman JA, Brunner HG. De novo mutations in human genetic disease. Nature Reviews Genetics 2012 13:8. Nature Publishing Group; 2012;13:565-565.

11. Wright CF, FitzPatrick DR, Firth HV. Paediatric genomics: diagnosing rare disease in children. Nature Reviews Genetics 2018 19:5. Nature Publishing Group; 2018;19:253-253.

12. Clark MM, Stark Z, Farnaes L, Tan TY, White SM, Dimmock D, et al. A meta-analysis of the diagnostic sensitivity and clinical utility of genome sequencing, exome sequencing and chromosomal microarray in children with suspected genetic diseases [Internet]. bioRxiv. 2018 [cited 2018 Jul 10]. p. 255299. Available from: https://www.biorxiv.org/content/early/2018/01/30/255299

13. 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, et al. A global reference for human genetic variation. Nature. 2015;526:68-74.

14. Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, et al. Analysis of proteincoding genetic variation in 60,706 humans. Nature. 2016;536:285-91.

15. Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP) [Internet]. Seattle, WA; [cited 2018 Jul 24]. Available from: http://evs.gs.washington.edu/EVS/

44 references, page 1 of 3
Abstract
<jats:title>Abstract</jats:title><jats:p>In the clinical setting, exome sequencing has become standard-of-care in diagnosing rare genetic disorders, however many patients remain unsolved. Trio sequencing has been demonstrated to produce a higher diagnostic yield than singleton (proband-only) sequencing. Parental sequencing is especially useful when a disease is suspected to be caused by a <jats:italic>de novo</jats:italic> variant in the proband, because parental data provide a strong filter for the majority of variants that are shared by the proband and their parents. However the additional cost of sequencing the parents makes the trio strategy uneconomical for...
Funded by
NHMRC| Harnessing the power of genomics to understand disease
Project
  • Funder: National Health and Medical Research Council (NHMRC) (NHMRC)
  • Project Code: 1126157
  • Funding stream: Career Development Fellowships
44 references, page 1 of 3

1. Glessner JT, Bick AG, Ito K, Homsy J, Rodriguez-Murillo L, Fromer M, et al. Increased frequency

2. Zaidi S, Choi M, Wakimoto H, Ma L, Jiang J, Overton JD, et al. De novo mutations in histonemodifying genes in congenital heart disease. Nature. 2013;498:220-3.

3. Brown TL, Meloche TM. Exome sequencing a review of new strategies for rare genomic disease research. Genomics. 2016;108:109-14.

4. Roach JC, Glusman G, Smit AFA, Huff CD, Hubley R, Shannon PT, et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science. 2010;328:636-9.

5. Clark MM, Stark Z, Farnaes L, Tan TY, White SM, Dimmock D, et al. Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases. npj Genomic Medicine. 2018;3:16.

6. de Ligt J, Willemsen MH, van Bon BWM, Kleefstra T, Yntema HG, Kroes T, et al. Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability. http://dx.doi.org/101056/NEJMoa1206524 [Internet]. Massachusetts Medical Society; 2012; Available from: https://www.nejm.org/doi/full/10.1056/nejmoa1206524

7. Rauch A, Wieczorek D, Graf E, Wieland T, Endele S, Schwarzmayr T, et al. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet. 2012;380:1674-82.

8. Vissers LELM, de Ligt J, Gilissen C, Janssen I, Steehouwer M, de Vries P, et al. A de novo paradigm for mental retardation. Nat Genet. 2010;42:1109-12. [OpenAIRE]

9. O'Roak BJ, Deriziotis P, Lee C, Vives L, Schwartz JJ, Girirajan S, et al. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet. 2011;43:585-9.

10. Veltman JA, Brunner HG. De novo mutations in human genetic disease. Nature Reviews Genetics 2012 13:8. Nature Publishing Group; 2012;13:565-565.

11. Wright CF, FitzPatrick DR, Firth HV. Paediatric genomics: diagnosing rare disease in children. Nature Reviews Genetics 2018 19:5. Nature Publishing Group; 2018;19:253-253.

12. Clark MM, Stark Z, Farnaes L, Tan TY, White SM, Dimmock D, et al. A meta-analysis of the diagnostic sensitivity and clinical utility of genome sequencing, exome sequencing and chromosomal microarray in children with suspected genetic diseases [Internet]. bioRxiv. 2018 [cited 2018 Jul 10]. p. 255299. Available from: https://www.biorxiv.org/content/early/2018/01/30/255299

13. 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, et al. A global reference for human genetic variation. Nature. 2015;526:68-74.

14. Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, et al. Analysis of proteincoding genetic variation in 60,706 humans. Nature. 2016;536:285-91.

15. Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP) [Internet]. Seattle, WA; [cited 2018 Jul 24]. Available from: http://evs.gs.washington.edu/EVS/

44 references, page 1 of 3
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