Posey JE, Rosenfeld JA, James RA, Bainbridge M, Niu Z, Wang X, Dhar S, Wiszniewski W, Akdemir ZH, Gambin T, et al. Molecular diagnostic experience of whole-exome sequencing in adult patients. Genet Med. 2016;18(7):678–85.
Article
CAS
Google Scholar
Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, et al. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med. 2013;369(16):1502–11.
Article
CAS
Google Scholar
Retterer K, Juusola J, Cho MT, Vitazka P, Millan F, Gibellini F, Vertino-Bell A, Smaoui N, Neidich J, Monaghan KG, et al. Clinical application of whole-exome sequencing across clinical indications. Genet Med. 2016;18(7):696–704.
Article
CAS
Google Scholar
Trujillano D, Bertoli-Avella AM, Kumar Kandaswamy K, Weiss ME, Koster J, Marais A, Paknia O, Schroder R, Garcia-Aznar JM, Werber M, et al. Clinical exome sequencing: results from 2819 samples reflecting 1000 families. Eur J Hum Genet. 2017;25(2):176–82.
Article
CAS
Google Scholar
Lee H, Deignan JL, Dorrani N, Strom SP, Kantarci S, Quintero-Rivera F, Das K, Toy T, Harry B, Yourshaw M, et al. Clinical exome sequencing for genetic identification of rare Mendelian disorders. Jama. 2014;312(18):1880–7.
Article
Google Scholar
Gilissen C, Hehir-Kwa JY, Thung DT, van de Vorst M, van Bon BW, Willemsen MH, Kwint M, Janssen IM, Hoischen A, Schenck A et al: Genome sequencing identifies major causes of severe intellectual disability. Nature 2014, 511(7509):344–347.
Article
CAS
Google Scholar
Willig LK, Petrikin JE, Smith LD, Saunders CJ, Thiffault I, Miller NA, Soden SE, Cakici JA, Herd SM, Twist G, et al. Whole-genome sequencing for identification of Mendelian disorders in critically ill infants: a retrospective analysis of diagnostic and clinical findings. Lancet Respir Med. 2015;3(5):377–87.
Article
CAS
Google Scholar
Schwarze K, Buchanan J, Taylor JC, Wordsworth S. Are whole-exome and whole-genome sequencing approaches cost-effective? Genet Med: A systematic review of the literature; 2018.
Google Scholar
Hannan AJ. Tandem repeats mediating genetic plasticity in health and disease. Nat Rev Genet. 2018;19(5):286–98.
Article
CAS
Google Scholar
Ashley EA. Towards precision medicine. Nat Rev Genet. 2016;17(9):507–22.
Article
CAS
Google Scholar
Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SFA, Hakonarson H, Bucan M. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007;17:1665–74.
Article
CAS
Google Scholar
Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, Bassett AS, Seller A, Holmes CC, Ragoussis J. QuantiSNP: an objective Bayes hidden-Markov model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res. 2007;35(6):2013–25.
Article
CAS
Google Scholar
Venkatraman ES, Olshen AB. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics. 2007;23(6):657–63.
Article
CAS
Google Scholar
Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. 2004;5(4):557–72.
Article
Google Scholar
Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet. 2011;12(5):363–76.
Article
CAS
Google Scholar
Merker JD, Wenger AM, Sneddon T, Grove M, Zappala Z, Fresard L, Waggott D, Utiramerur S, Hou Y, Smith KS, et al. Long-read genome sequencing identifies causal structural variation in a Mendelian disease. Genet Med. 2017.
Kirby A, Gnirke A, Jaffe DB, Baresova V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, et al. Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing. Nat Genet. 2013;45(3):299–303.
Article
CAS
Google Scholar
Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC: Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods 2018, 15(6):461–468.
Sanchis-Juan A, Stephens J, French CE, Gleadall N, Mégy K, Penkett C, Stirrups K, Delon I, Dewhurst E, Dolling H, et al. Complex structural variants resolved by short-read and long-read whole genome sequencing in Mendelian disorders. BioRxiv. 2018. https://doi.org/10.1101/281683.
Liu Q, Zhang P, Wang D, Gu W, Wang K. Interrogating the "unsequenceable" genomic trinucleotide repeat disorders by long-read sequencing. Genome Med. 2017;9(1):65.
Article
Google Scholar
Loomis EW, Eid JS, Peluso P, Yin J, Hickey L, Rank D, McCalmon S, Hagerman RJ, Tassone F, Hagerman PJ. Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene. Genome Res. 2013;23(1):121–8.
Article
CAS
Google Scholar
Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X, Fu A, Li Q, Li N, Gong S, et al. Long-read sequencing and de novo assembly of a Chinese genome. Nat Commun. 2016;7:12065.
Article
CAS
Google Scholar
Seo JS, Rhie A, Kim J, Lee S, Sohn MH, Kim CU, Hastie A, Cao H, Yun JY, Kim J, et al. De novo assembly and phasing of a Korean human genome. Nature. 2016;538(7624):243–7.
Article
CAS
Google Scholar
Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018;36(4):338–45.
Article
CAS
Google Scholar
Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stutz AM, Stedman W, Anantharaman T, Hastie A, et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods. 2015;12(8):780–6.
Article
CAS
Google Scholar
Chou JY, Mansfield BC. Mutations in the glucose-6-phosphatase-alpha (G6PC) gene that cause type Ia glycogen storage disease. Hum Mutat. 2008;29(7):921–30.
Article
CAS
Google Scholar
Zheng BX, Lin Q, Li M, Jin Y. Three novel mutations of the G6PC gene identified in Chinese patients with glycogen storage disease type Ia. Eur J Pediatr. 2015;174(1):59–63.
Article
CAS
Google Scholar
Kishnani PS, Austin SL, Abdenur JE, Arn P, Bali DS, Boney A, Chung WK, Dagli AI, Dale D, Koeberl D, et al. Diagnosis and management of glycogen storage disease type I: a practice guideline of the American College of Medical Genetics and Genomics. Genetics in medicine : official journal of the American College of Medical Genetics. 2014;16(11):e1.
Article
CAS
Google Scholar
Matern D, Seydewitz HH, Bali D, Lang C, Chen YT. Glycogen storage disease type I: diagnosis and phenotype/genotype correlation. Eur J Pediatr. 2002;161(Suppl 1):S10–9.
Article
CAS
Google Scholar
Chou JY, Jun HS, Mansfield BC. Type I glycogen storage diseases: disorders of the glucose-6-phosphatase/glucose-6-phosphate transporter complexes. J Inherit Metab Dis. 2015;38(3):511–9.
Article
CAS
Google Scholar
Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC. Accurate detection of complex structural variations using single molecule sequencing. Nat Methods. 2018;15(6):461–468.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. Genome project data processing S: the sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
Google Scholar
Maria, Nattestad C-SC, Schatz MC. Ribbon: Visualizing complex genome alignments and structural variation. bioRxiv. 2016. https://doi.org/10.1101/082123.
Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178–92.
Article
CAS
Google Scholar
Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16):e164.
Article
Google Scholar
Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405–24.
Article
Google Scholar
Li Q, Wang K. InterVar: clinical interpretation of genetic variants by the 2015 ACMG-AMP guidelines. Am J Hum Genet. 2017;100(2):267–80.
Article
CAS
Google Scholar
Alpha Scientists in Reproductive Medicine and ESHRE Special Interest Group of Embryology. The Istanbul consensus workshop on embryo assessment: proceedings of an expert meeting. Hum Reprod. 2011;26(6):1270–83.
Ade C, Roy-Engel AM, Deininger PL. Alu elements: an intrinsic source of human genome instability. Current opinion in virology. 2013;3(6):639–45.
Article
CAS
Google Scholar
Sen SK, Han K, Wang J, Lee J, Wang H, Callinan PA, Dyer M, Cordaux R, Liang P, Batzer MA. Human genomic deletions mediated by recombination between Alu elements. Am J Hum Genet. 2006;79(1):41–53.
Article
CAS
Google Scholar
Kim S, Cho CS, Han K, Lee J. Structural variation of Alu element and human disease. Genomics Inform. 2016;14(3):70–7.
Article
Google Scholar
Lei KJ, Shelly LL, Pan CJ, Sidbury JB, Chou JY. Mutations in the glucose-6-phosphatase gene that cause glycogen storage disease type 1a. Science. 1993;262(5133):580–3.
Article
CAS
Google Scholar
Chou JY, Jun HS, Mansfield BC. Glycogen storage disease type I and G6Pase-beta deficiency: etiology and therapy. Nat Rev Endocrinol. 2010;6(12):676–88.
Article
CAS
Google Scholar
Gu LL, Li XH, Han Y, Zhang DH, Gong QM, Zhang XX. A novel homozygous no-stop mutation in G6PC gene from a Chinese patient with glycogen storage disease type Ia. Gene. 2014;536(2):362–5.
Article
CAS
Google Scholar
Wang Q, Shashikant CS, Jensen M, Altman NS, Girirajan S. Novel metrics to measure coverage in whole exome sequencing datasets reveal local and global non-uniformity. Sci Rep. 2017;7(1):885.
Article
Google Scholar