References

1.
Mendel G. Versuche über pflanzenhybriden. Verh Naturf Ver Brünn. 1866;4:3—47.
2.
Miescher F. Über die chemische zusammensetzung der eiterzellen. Hoppe-Seyler’s Med Chem Unters. 1871;4:441-460.
3.
Miescher F. Das protamin, eine neue organische basis aus den samenfäden des rheinlachses. Ber Deutsch Chem Ges. 1874;7:376—379.
4.
Miescher F. Die spermatozoen einiger wilbertiere. Ein Beitrag zur histochemie Verh Naturf Ges. 1874;6:138—208.
5.
Kossel A, Neumann A. Über das thymin, ein spaltungsprodukt der nukleinsäure. Ber Deutsch Chem Ges. 1893;26:2753—2756.
6.
Flemming W. Zur kenntniss der zelle und ihrer theilungs-erscheinungen. Schriften des Naturwissenschaftlichen Vereins für Schleswig-Holstein. 1878;3:23—27.
7.
Boveri TH. Über mehrpolige mitosen als mittel zur analyse des zellkerns. Verh Phys Med Ges Vürzb. 1902;35:60-90.
8.
Boveri TH. Über die konstitution der chromatischen kernsubstanz. Verh Deutsch Zool Ges Würzb. 1903;13(10–33).
9.
Sutton WS. The chromosomes in heredity. Biol Bull (Woods Hole). 1903;4:231-251.
10.
Avery OT, Macleod CM, McCarty M. STUDIES ON THE CHEMICAL NATURE OF THE SUBSTANCE INDUCING TRANSFORMATION OF PNEUMOCOCCAL TYPES : INDUCTION OF TRANSFORMATION BY a DESOXYRIBONUCLEIC ACID FRACTION ISOLATED FROM PNEUMOCOCCUS TYPE III. J Exp Med. 1944;79(2):137-158.
11.
Chargaff E, Vischer E, Doniger R, Green C, Misani F. The composition of the desoxypentose nucleic acids of thymus and spleen. J Biol Chem. 1949;177(1):405-416.
12.
FRANKLIN RE, GOSLING RG. Molecular configuration in sodium thymonucleate. Nature. 1953;171(4356):740-741.
13.
WATSON JD, CRICK FH. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature. 1953;171(4356):737-738.
14.
CRICK FH. On protein synthesis. Symp Soc Exp Biol. 1958;12:138-163.
15.
Crick F. Central dogma of molecular biology. Nature. 1970;227(5258):561-563.
16.
TJIO JH, LEVAN A. THE CHROMOSOME NUMBER OF MAN. Hereditas. 1956;42(1‐2):1-6.
17.
Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860-921.
18.
Gu W, Zhang F, Lupski JR. Mechanisms for human genomic rearrangements. Pathogenetics. 2008;1(1):4.
19.
Sanger F, Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol. 1975;94(3):441-448.
20.
Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977;74(2):560-564.
21.
Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977;74(12):5463-5467.
22.
Nyrén P, Lundin A. Enzymatic method for continuous monitoring of inorganic pyrophosphate synthesis. Anal Biochem. 1985;151(2):504-509.
23.
Ronaghi M, Uhlén M, Nyrén P. A sequencing method based on real-time pyrophosphate. Science. 1998;281(5375):363, 365.
24.
Li Z, Bai X, Ruparel H, Kim S, Turro NJ, Ju J. A photocleavable fluorescent nucleotide for DNA sequencing and analysis. Proc Natl Acad Sci U S A. 2003;100(2):414-419.
25.
Fedurco M, Romieu A, Williams S, Lawrence I, Turcatti G. BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res. 2006;34(3):e22.
26.
Turcatti G, Romieu A, Fedurco M, Tairi A-P. A new class of cleavable fluorescent nucleotides: Synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res. 2008;36(4):e25.
27.
Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988;85(8):2444-2448.
28.
Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM. The sanger FASTQ file format for sequences with quality scores, and the solexa/illumina FASTQ variants. Nucleic Acids Res. 2010;38(6):1767-1771.
29.
Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078-2079.
30.
Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol. 1981;147(1):195-197.
31.
Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970;48(3):443-453.
32.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403-410.
33.
Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform. 2010;11(5):473-483.
34.
Burrows M, Wheeler DJ. A Block-Sorting Lossless Data Compression Algorithm.; 1994.
35.
Lam TW, Sung WK, Tam SL, Wong CK, Yiu SM. Compressed indexing and local alignment of DNA. Bioinformatics. 2008;24(6):791-797.
36.
Li H, Durbin R. Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics. 2010;26(5):589-595.
37.
McKenna A, Hanna M, Banks E, et al. The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-1303.
38.
DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43(5):491-498.
39.
Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27(21):2987-2993.
40.
Van der Auwera GA, Carneiro MO, Hartl C, et al. From FastQ data to high confidence variant calls: The genome analysis toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;43(1110):11.10.1-11.10.33.
41.
Poplin R, Ruano-Rubio V, DePristo MA, et al. Scaling accurate genetic variant discovery to tens of thousands of samples. bioRxiv. Published online 2018.
42.
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. Published online 2012.
43.
Chen J, Li X, Zhong H, Meng Y, Du H. Systematic comparison of germline variant calling pipelines cross multiple next-generation sequencers. Sci Rep. 2019;9(1):9345.
44.
Xu C. A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data. Comput Struct Biotechnol J. 2018;16:15-24.
45.
Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011;21(6):974-984.
46.
Plagnol V, Curtis J, Epstein M, et al. A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics. 2012;28(21):2747-2754.
47.
Korbel JO, Urban AE, Affourtit JP, et al. Paired-end mapping reveals extensive structural variation in the human genome. Science. 2007;318(5849):420-426.
48.
Layer RM, Chiang C, Quinlan AR, Hall IM. LUMPY: A probabilistic framework for structural variant discovery. Genome Biol. 2014;15(6):R84.
49.
Zhu M, Need AC, Han Y, et al. Using ERDS to infer copy-number variants in high-coverage genomes. Am J Hum Genet. 2012;91(3):408-421.
50.
Auton A, Brooks LD, Durbin RM, et al. A global reference for human genetic variation. Nature. 2015;526(7571):68-74.
51.
Sherry ST, Ward M, Sirotkin K. dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res. 1999;9(8):677-679.
52.
Mailman MD, Feolo M, Jin Y, et al. The NCBI dbGaP database of genotypes and phenotypes. Nat Genet. 2007;39(10):1181-1186.
53.
Landrum MJ, Lee JM, Riley GR, et al. ClinVar: Public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42(Database issue):D980-5.
54.
Hubbard T, Barker D, Birney E, et al. The ensembl genome database project. Nucleic Acids Res. 2002;30(1):38-41.
55.
Yates AD, Achuthan P, Akanni W, et al. Ensembl 2020. Nucleic Acids Res. 2020;48(D1):D682-D688.
56.
McLaren W, Gil L, Hunt SE, et al. The ensembl variant effect predictor. Genome Biol. 2016;17(1):122.
57.
Karczewski KJ, Francioli LC, Tiao G, et al. Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes. bioRxiv. Published online 2019.
58.
Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet. 2013;Chapter 7:Unit7.20.
59.
Jager M, Wang K, Bauer S, Smedley D, Krawitz P, Robinson PN. Jannovar: A java library for exome annotation. Hum Mutat. 2014;35(5):548-555.
60.
Harper PS. A Short History of Medical Genetics. Oxford University Press USA - OSO; 2008.
61.
Garrod AE. THE INCIDENCE OF ALKAPTONURIA : A STUDY IN CHEMICAL INDIVIDUALITY. The Lancet. 1902;160(4137):1616-1620.
62.
Garrod AE. Inborn Errors of Metabolism. Oxford University Press; 1923.
63.
Garrod AE. Inborn Factors of Disease: An Essay. Clarendon Press; 1931.
64.
Rimoin DL, Hirschhorn K. A history of medical genetics in pediatrics. Pediatr Res. 2004;56(1):150-159.
65.
Fisher RA. XV.—the correlation between relatives on the supposition of mendelian inheritance. Transactions of the Royal Society of Edinburgh. 1919;52(2):399-433.
66.
LEVAN A. THE EFFECT OF COLCHICINE ON ROOT MITOSES IN ALLIUM. Hereditas. 1938;24(4):471-486.
67.
Caspersson T, Zech L, Johansson C, Modest EJ. Identification of human chromosomes by DNA-binding fluorescent agents. Chromosoma. 1970;30(2):215-227.
68.
Seabright M. A rapid banding technique for human chromosomes. Lancet. 1971;2(7731):971-972.
69.
Fan YS, Davis LM, Shows TB. Mapping small DNA sequences by fluorescence in situ hybridization directly on banded metaphase chromosomes. Proc Natl Acad Sci U S A. 1990;87(16):6223-6227.
70.
Danna K, Nathans D. Specific cleavage of simian virus 40 DNA by restriction endonuclease of hemophilus influenzae. Proc Natl Acad Sci U S A. 1971;68(12):2913-2917.
71.
Southern EM. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975;98(3):503-517.
72.
Shine J, Seeburg PH, Martial JA, Baxter JD, Goodman HM. Construction and analysis of recombinant DNA for human chorionic somatomammotropin. Nature. 1977;270(5637):494-499.
73.
Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980;32(3):314-331.
74.
Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H. Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction. Cold Spring Harb Symp Quant Biol. 1986;51 Pt 1:263-273.
75.
GUTHRIE R, SUSI A. A SIMPLE PHENYLALANINE METHOD FOR DETECTING PHENYLKETONURIA IN LARGE POPULATIONS OF NEWBORN INFANTS. Pediatrics. 1963;32:338-343.
76.
JERVIS GA. Phenylpyruvic oligophrenia deficiency of phenylalanine-oxidizing system. Proc Soc Exp Biol Med. 1953;82(3):514-515.
77.
BICKEL H, GERRARD J, HICKMANS EM. Influence of phenylalanine intake on phenylketonuria. Lancet. 1953;265(6790):812-813.
78.
FUCHS F, RIIS P. Antenatal sex determination. Nature. 1956;177(4503):330.
79.
Steele MW, Breg WRJ. Chromosome analysis of human amniotic-fluid cells. Lancet. 1966;1(7434):383-385.
80.
Walknowska J, Conte FA, Grumbach MM. Practical and theoretical implications of fetal-maternal lymphocyte transfer. Lancet. 1969;1(7606):1119-1122.
81.
Mueller UW, Hawes CS, Wright AE, et al. Isolation of fetal trophoblast cells from peripheral blood of pregnant women. Lancet. 1990;336(8709):197-200.
82.
Bianchi DW, Flint AF, Pizzimenti MF, Knoll JH, Latt SA. Isolation of fetal DNA from nucleated erythrocytes in maternal blood. Proc Natl Acad Sci U S A. 1990;87(9):3279-3283.
83.
Lo YM, Corbetta N, Chamberlain PF, et al. Presence of fetal DNA in maternal plasma and serum. Lancet. 1997;350(9076):485-487.
84.
Scotchman E, Chandler NJ, Mellis R, Chitty LS. Noninvasive prenatal diagnosis of single-gene diseases: The next frontier. Clin Chem. 2020;66(1):53-60.
85.
Marchuk DS, Crooks K, Strande N, et al. Increasing the diagnostic yield of exome sequencing by copy number variant analysis. PLoS One. 2018;13(12):e0209185.
86.
Retterer K, Scuffins J, Schmidt D, et al. Assessing copy number from exome sequencing and exome array CGH based on CNV spectrum in a large clinical cohort. Genet Med. 2015;17(8):623-629.
87.
Yao R, Zhang C, Yu T, et al. Evaluation of three read-depth based CNV detection tools using whole-exome sequencing data. Mol Cytogenet. 2017;10:30.
88.
Fromer M, Moran JL, Chambert K, et al. Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. Am J Hum Genet. 2012;91(4):597-607.
89.
Jiang Y, Oldridge DA, Diskin SJ, Zhang NR. CODEX: A normalization and copy number variation detection method for whole exome sequencing. Nucleic Acids Res. 2015;43(6):e39.
90.
Krumm N, Sudmant PH, Ko A, et al. Copy number variation detection and genotyping from exome sequence data. Genome Res. 2012;22(8):1525-1532.
91.
Truty R, Paul J, Kennemer M, et al. Prevalence and properties of intragenic copy-number variation in mendelian disease genes. Genet Med. 2019;21(1):114-123.
92.
Benjamini Y, Speed TP. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res. 2012;40(10):e72.
93.
Kadalayil L, Rafiq S, Rose-Zerilli MJJ, et al. Exome sequence read depth methods for identifying copy number changes. Brief Bioinform. 2015;16(3):380-392.
94.
Chiang DY, Getz G, Jaffe DB, et al. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods. 2009;6(1):99-103.
95.
Foreman AKM, Lee K, Evans JP. The NCGENES project: Exploring the new world of genome sequencing. N C Med J. 2013;74(6):500-504.
96.
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Published online 2013.
97.
Koster J, Rahmann S. Snakemake–a scalable bioinformatics workflow engine. Bioinformatics. 2012;28(19):2520-2522.
98.
Trost B, Walker S, Wang Z, et al. A comprehensive workflow for read depth-based identification of copy-number variation from whole-genome sequence data. Am J Hum Genet. 2018;102(1):142-155.
99.
Yu D, Huber W, Vitek O. Shrinkage estimation of dispersion in negative binomial models for RNA-seq experiments with small sample size. Bioinformatics. 2013;29(10):1275-1282.
100.
Benjamini Y, Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B (Methodological). 1995;57(1):289-300.
101.
Minka TP. Estimating a Dirichlet Distribution.; 2000.
102.
Matthews BW. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta. 1975;405(2):442-451.
103.
Neiman M, Sundling S, Grönberg H, et al. Library preparation and multiplex capture for massive parallel sequencing applications made efficient and easy. PLOS ONE. 2012;7(11):1-6.
104.
Ramos E, Levinson BT, Chasnoff S, et al. Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing. BMC Genomics. 2012;13:683.
105.
Rohland N, Reich D. Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res. 2012;22(5):939-946.
106.
Wesolowska A, Dalgaard MD, Borst L, et al. Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia. Leukemia. 2011;25(6):1001-1006.
107.
Shearer AE, Hildebrand MS, Ravi H, et al. Pre-capture multiplexing improves efficiency and cost-effectiveness of targeted genomic enrichment. BMC Genomics. 2012;13:618.
108.
Mackie FL, Hemming K, Allen S, Morris RK, Kilby MD. The accuracy of cell-free fetal DNA-based non-invasive prenatal testing in singleton pregnancies: A systematic review and bivariate meta-analysis. BJOG. 2017;124(1):32-46.
109.
Zhang J, Li J, Saucier JB, et al. Non-invasive prenatal sequencing for multiple mendelian monogenic disorders using circulating cell-free fetal DNA. Nat Med. Published online January 2019.
110.
Tsao DS, Silas S, Landry BP, et al. A novel high-throughput molecular counting method with single base-pair resolution enables accurate single-gene NIPT. Sci Rep. 2019;9(1):14382.
111.
Lo YMD, Chan KCA, Sun H, et al. Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci Transl Med. 2010;2(61):61ra91.
112.
Hui WWI, Jiang P, Tong YK, et al. Universal haplotype-based noninvasive prenatal testing for single gene diseases. Clin Chem. 2017;63(2):513-524.
113.
Jang SS, Lim BC, Yoo S-K, et al. Targeted linked-read sequencing for direct haplotype phasing of maternal DMD alleles: A practical and reliable method for noninvasive prenatal diagnosis. Sci Rep. 2018;8(1):8678.
114.
Vermeulen C, Geeven G, Wit E de, et al. Sensitive monogenic noninvasive prenatal diagnosis by targeted haplotyping. Am J Hum Genet. 2017;101(3):326-339.
115.
Chandler NJ, Ahlfors H, Drury S, et al. Noninvasive prenatal diagnosis for cystic fibrosis: Implementation, uptake, outcome, and implications. Clin Chem. 2020;66(1):207-216.
116.
Salomon LJ, Sotiriadis A, Wulff CB, Odibo A, Akolekar R. Risk of miscarriage following amniocentesis or chorionic villus sampling: Systematic review of literature and updated meta-analysis. Ultrasound Obstet Gynecol. 2019;54(4):442-451.
117.
Fan HC, Gu W, Wang J, Blumenfeld YJ, El-Sayed YY, Quake SR. Non-invasive prenatal measurement of the fetal genome. Nature. 2012;487(7407):320-324.
118.
Kitzman JO, Snyder MW, Ventura M, et al. Noninvasive whole-genome sequencing of a human fetus. Sci Transl Med. 2012;4(137):137ra76.
119.
Snyder MW, Simmons LE, Kitzman JO, et al. Noninvasive fetal genome sequencing: A primer. Prenat Diagn. 2013;33(6):547-554.
120.
Seaby EG, Pengelly RJ, Ennis S. Exome sequencing explained: A practical guide to its clinical application. Brief Funct Genomics. 2016;15(5):374-384.
121.
R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing; 2019.
122.
Chan KCA, Zhang J, Hui ABY, et al. Size distributions of maternal and fetal DNA in maternal plasma. Clin Chem. 2004;50(1):88-92.
123.
Chan KCA, Jiang P, Sun K, et al. Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends. Proc Natl Acad Sci U S A. 2016;113(50):E8159-E8168.
124.
Jiang P, Lo YMD. The long and short of circulating cell-free DNA and the ins and outs of molecular diagnostics. Trends Genet. 2016;32(6):360-371.
125.
Rabinowitz T, Polsky A, Golan D, et al. Bayesian-based noninvasive prenatal diagnosis of single-gene disorders. Genome Res. 2019;29(3):428-438.
126.
Kinnings SL, Geis JA, Almasri E, et al. Factors affecting levels of circulating cell-free fetal DNA in maternal plasma and their implications for noninvasive prenatal testing. Prenat Diagn. 2015;35(8):816-822.