Robust Diagnostic Genetic Testing Using Solution Capture Enrichment and a Novel Variant-Filtering Interface

Human Mutation

Volumn 35, Issue 4, 2014, Pages 434-441

  Watson, Christopher M ^a   Crinnion, Laura A ^a   Morgan, Joanne E ^b   Harrison, Sally M ^b   Diggle, Christine P ^b   Adlard, Julian ^a   Lindsay, Helen A ^a   Camm, Nick ^a   Charlton, Ruth ^a   Sheridan, Eamonn ^b   Bonthron, David T ^b   Taylor, Graham R ^c   Carr, Ian M ^b  

^a ST JAMES S UNIVERSITY HOSPITAL   (United Kingdom)

^b UNIVERSITY OF LEEDS   (United Kingdom)

^c UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Exome sequencing; Mutation detection; Sequence analysis; Software

Indexed keywords

ARTICLE; CLINICAL ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; DNAH8 GENE; DYSKINESIA; FAMILIAL CANCER; GENE; GENE MUTATION; GENE SEQUENCE; GENETIC SCREENING; GENETIC VARIABILITY; GENOTYPE; HUMAN; PRIORITY JOURNAL; GENETIC PREDISPOSITION; GENETIC VARIATION; GENETICS; HIGH THROUGHPUT SEQUENCING; KARTAGENER SYNDROME; NEOPLASMS; PROCEDURES; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM; SOFTWARE; STOP CODON; TUMOR GENE;

AXONEMAL DYNEIN; DYNEIN ADENOSINE TRIPHOSPHATASE; STOP CODON;

AXONEMAL DYNEINS; CODON, NONSENSE; DYNEINS; GENES, NEOPLASM; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; KARTAGENER SYNDROME; NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84896137851     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22490     Document Type: Article

References (18)

1. Antony D, Becker-Heck A, Zariwala MA, Schmidts M, Onoufriadis A, Forouhan M, Wilson R, Taylor-Cox T, Dewar A, Jackson C, Goggin P, Loges NT, et al. 2013. Mutations in CCDC39 and CCDC40 are the major cause of primary ciliary dyskinesia with axonemal disorganization and absent inner dynein arms. Hum Mutat 34:462-472.
2. Carr IM, Bhaskar S, O'Sullivan J, Aldahmesh MA, Shamseldin HE, Markham AF, Bonthron DT, Black G, Alkuraya FS. 2013. Autozygosity mapping with exome sequence data. Hum Mutat 34:50-56.
3. Carr IM, Flintoff KJ, Taylor GR, Markham AF, Bonthron DT. 2006. Interactive visual analysis of SNP data for rapid autozygosity mapping in consanguineous families. Hum Mutat 27:1041-1046.
4. Chaki M, Gee HY, Otto EA, Diaz K, Hurd TW, Halbritter J, Allen SJ, Zariwala MB, Knowles MR, Hildebrandt F. Whole exome resequencing identifies mutations in LRRC6 as a novel single-gene cause of primary cliary dyskinesia. (Abstract/Program #406). Presented at the 62nd Annual Meeting of The American Society of Human Genetics, San Francisco.
5. DePristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C, Philippakis A, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell T, et al. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491-498.
6. Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT. 2011. LOVD v.2.0: the next generation in gene variant databases. Hum Mutat 32:557-563.
7. Jiang Y, Wang Y, Brudno M. 2012. PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinformatics 28:2576-2583.
8. Karuman P, Gozani O, Odze RD, Zhou XC, Zhu H, Shaw R, Brien TP, Bozzuto CD, Ooi D, Cantley LC, Yuan J. 2001. The Peutz-Jegher gene product LKB1 is a mediator of p53-dependent cell death. Mol Cell 7:1307-1319.
9. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
10. Morgan JE, Carr IM, Sheridan E, Chu CE, Hayward B, Camm N, Lindsay HA, Mattocks CJ, Markham AF, Bonthron DT, Taylor GR. 2010. Genetic diagnosis of familial breast cancer using clonal sequencing. Hum Mutat 31:484-491.
11. O'Sullivan J, Mullaney BG, Bhaskar SS, Dickerson JE, Hall G, O'Grady A, Webster A, Ramsden SC, Black GC. 2012. A paradigm shift in the delivery of services for diagnosis of inherited retinal disease. J Med Genet 49:322-326.
12. Pazour GJ, Agrin N, Walker BL, Witman GB. 2006. Identification of predicted human outer dynein arm genes: candidates for primary ciliary dyskinesia genes. J Med Genet 43:62-73.
13. Shendure J, Lieberman Aiden E. 2012. The expanding scope of DNA sequencing. Nat Biotechnol 30:1084-1094.
14. Shi Y, Majewski J. 2013. FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data. Bioinformatics 29:1461-1462.
15. Sikkema-Raddatz B, Johansson LF, de Boer EN, Almomani R, Boven LG, van den Berg MP, van Spaendonck-Zwarts KY, van Tintelen JP, Sijmons RH, Jongbloed JD, Sinke RJ. 2013. Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics. Hum Mutat 34:10351042.
16. Thorvaldsdóttir H, Robinson JT, Mesirov JP. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178-192.
17. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. 2009. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25:2865-2871.
18. Zariwala MA, Leigh MW, Ceppa F, Kennedy MP, Noone PG, Carson JL, Hazucha MJ, Lori A, Horvath J, Olbrich H, Loges NT, Bridoux AM, et al. 2006. Mutations of DNAI1 in primary ciliary dyskinesia: evidence of founder effect in a common mutation. Am J Respir Crit Care Med 174:858-866.