Next-Generation Molecular Testing of Newborn Dried Blood Spots for Cystic Fibrosis

Journal of Molecular Diagnostics

Volumn 18, Issue 2, 2016, Pages 267-282

  Lefterova, Martina I ^a   Shen, Peidong ^a   Odegaard, Justin I ^a   Fung, Eula ^a   Chiang, Tsoyu ^a   Peng, Gang ^c   Davis, Ronald W ^a   Wang, Wenyi ^c   Kharrazi, Martin ^d   Schrijver, Iris ^a,b   Scharfe, Curt ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b STANFORD UNIVERSITY MEDICAL CENTER   (United States)

^c UNIVERSITY OF TEXAS   (United States)

^d CALIFORNIA DEPARTMENT OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR; GENOMIC DNA; CFTR PROTEIN, HUMAN; PRIMER DNA;

AMPLICON; ARTICLE; COST CONTROL; COST EFFECTIVENESS ANALYSIS; CYSTIC FIBROSIS; DNA EXTRACTION; DRIED BLOOD SPOT TESTING; EXON; GENE FREQUENCY; HIGH THROUGHPUT SCREENING; HUMAN; INDEL MUTATION; INTRON; MAJOR CLINICAL STUDY; MOLECULAR DIAGNOSIS; MULTIPLEX POLYMERASE CHAIN REACTION; NEWBORN; NEWBORN SCREENING; NEXT GENERATION SEQUENCING; PREDICTIVE VALUE; SINGLE NUCLEOTIDE POLYMORPHISM; COPY NUMBER VARIATION; COST; ECONOMICS; GENETIC SCREENING; GENETICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; QUALITY CONTROL; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY;

COSTS AND COST ANALYSIS; CYSTIC FIBROSIS; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR; DNA COPY NUMBER VARIATIONS; DNA PRIMERS; DRIED BLOOD SPOT TESTING; GENETIC TESTING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFANT, NEWBORN; MULTIPLEX POLYMERASE CHAIN REACTION; NEONATAL SCREENING; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 84960811674     PISSN: 15251578     EISSN: 19437811     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2015.11.005     Document Type: Article

References (42)

1. I. Schrijver Mutation distribution in expanded screening for cystic fibrosis: making up the balance in a context of ethnic diversity Clin Chem 57 2011 799 801
2. G.R. Cutting Cystic fibrosis genetics: from molecular understanding to clinical application Nat Rev Genet 16 2015 45 56
3. J. Zielenski Genotype and phenotype in cystic fibrosis Respiration 67 2000 117 133
4. P.R. Sosnay, K.R. Siklosi, F. Van Goor, K. Kaniecki, H. Yu, N. Sharma, A.S. Ramalho, M.D. Amaral, R. Dorfman, J. Zielenski, D.L. Masica, R. Karchin, L. Millen, P.J. Thomas, G.P. Patrinos, M. Corey, M.H. Lewis, J.M. Rommens, C. Castellani, C.M. Penland, and G.R. Cutting Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene Nat Genet 45 2013 1160 1167
5. S.D. Grosse, C.A. Boyle, J.R. Botkin, A.M. Comeau, M. Kharrazi, M. Rosenfeld, B.S. Wilfond CDC Newborn screening for cystic fibrosis: evaluation of benefits and risks and recommendations for state newborn screening programs MMWR Recomm Rep 53 RR-13 2004 1 36
6. F.N. Dijk, and D.A. Fitzgerald The impact of newborn screening and earlier intervention on the clinical course of cystic fibrosis Paediatr Respir Rev 13 2012 220 225
7. J.S. Wagener, E.T. Zemanick, and M.K. Sontag Newborn screening for cystic fibrosis Curr Opin Pediatr 24 2012 329 335
8. L. Prach, R. Koepke, M. Kharrazi, S. Keiles, D.B. Salinas, M.C. Reyes, M. Pian, H. Opsimos, K.N. Otsuka, K.A. Hardy, C.E. Milla, J.M. Zirbes, B. Chipps, S. O'Bra, M.M. Saeed, R. Sudhakar, S. Lehto, D. Nielson, G.F. Shay, M. Seastrand, S. Jhawar, B. Nickerson, C. Landon, A. Thompson, E. Nussbaum, T. Chin, H. Wojtczak California Cystic Fibrosis Newborn Screening Consortium Novel CFTR variants identified during the first 3 years of cystic fibrosis newborn screening in California J Mol Diagn 15 2013 710 722
9. C.L. Ren, A.K. Fink, K. Petren, D.S. Borowitz, S.A. McColley, D.B. Sanders, M. Rosenfeld, and B.C. Marshall Outcomes of infants with indeterminate diagnosis detected by cystic fibrosis newborn screening Pediatrics 135 2015 e1386 e1392
10. M. Kharrazi, J. Yang, T. Bishop, S. Lessing, S. Young, S. Graham, M. Pearl, H. Chow, T. Ho, R. Currier, L. Gaffney, and L. Feuchtbaum Newborn screening for cystic fibrosis in California Pediatrics 136 2015 1062 1072
11. D. Trujillano, M.D. Ramos, J. Gonzalez, C. Tornador, F. Sotillo, G. Escaramis, S. Ossowski, L. Armengol, T. Casals, and X. Estivill Next generation diagnostics of cystic fibrosis and CFTR-related disorders by targeted multiplex high-coverage resequencing of CFTR J Med Genet 50 2013 455 462
12. A.N. Abou Tayoun, C.D. Tunkey, T.J. Pugh, T. Ross, M. Shah, C.C. Lee, T.T. Harkins, W.A. Wells, L.J. Tafe, C.I. Amos, and G.J. Tsongalis A comprehensive assay for CFTR mutational analysis using next-generation sequencing Clin Chem 59 2013 1481 1488
13. D.S. Grosu, L. Hague, M. Chelliserry, K.M. Kruglyak, R. Lenta, B. Klotzle, J. San, W.M. Goldstein, S. Moturi, P. Devers, J. Woolworth, E. Peters, B. Elashoff, J. Stoerker, D.J. Wolff, K.J. Friedman, W.E. Highsmith, E. Lin, and F.S. Ong Clinical investigational studies for validation of a next-generation sequencing in vitro diagnostic device for cystic fibrosis testing Expert Rev Mol Diagn 14 2014 605 622
14. C.A. Saavedra-Matiz, J.T. Isabelle, C.K. Biski, S.J. Duva, M.L. Sweeney, A.L. Parker, A.J. Young, L.L. Diantonio, L.M. Krein, M.J. Nichols, and M. Caggana Cost-effective and scalable DNA extraction method from dried blood spots Clin Chem 59 2013 1045 1051
15. M.W. Baker, A.E. Atkins, S.K. Cordovado, M. Hendrix, M.C. Earley, and P.M. Farrell Improving newborn screening for cystic fibrosis using next-generation sequencing technology: a technical feasibility study Genet Med 2015 [Epub ahead of print] doi: 10.1038/gim.2014.209
16. S. Rozen, and H. Skaletsky Primer3 on the WWW for general users and for biologist programmers Methods Mol Biol 132 2000 365 386
17. P.J. Cock, T. Antao, J.T. Chang, B.A. Chapman, C.J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski, and M.J. de Hoon Biopython: freely available Python tools for computational molecular biology and bioinformatics Bioinformatics 25 2009 1422 1423
18. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
19. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools Bioinformatics 25 2009 2078 2079
20. A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, and M.A. DePristo The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data Genome Res 20 2010 1297 1303
21. M.A. DePristo, E. Banks, R. Poplin, K.V. Garimella, J.R. Maguire, C. Hartl, A.A. Philippakis, G. del Angel, M.A. Rivas, M. Hanna, A. McKenna, T.J. Fennell, A.M. Kernytsky, A.Y. Sivachenko, K. Cibulskis, S.B. Gabriel, D. Altshuler, and M.J. Daly A framework for variation discovery and genotyping using next-generation DNA sequencing data Nat Genet 43 2011 491 498
22. Garrison E, Marth G: Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012
23. K. Wang, M. Li, and H. Hakonarson ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data Nucleic Acids Res 38 2010 e164
24. V. Plagnol, J. Curtis, M. Epstein, K.Y. Mok, E. Stebbings, S. Grigoriadou, N.W. Wood, S. Hambleton, S.O. Burns, A.J. Thrasher, D. Kumararatne, R. Doffinger, and S. Nejentsev A robust model for read count data in exome sequencing experiments and implications for copy number variant calling Bioinformatics 28 2012 2747 2754
25. J. Li, R. Lupat, K.C. Amarasinghe, E.R. Thompson, M.A. Doyle, G.L. Ryland, R.W. Tothill, S.K. Halgamuge, I.G. Campbell, and K.L. Gorringe CONTRA: copy number analysis for targeted resequencing Bioinformatics 28 2012 1307 1313
26. W.S. Cleveland LOWESS: a program for smoothing scatterplots by robust locally weighted regression Am Stat 35 1981
27. I. Schrijver, L.M. Pique, S. Graham, M. Pearl, A. Cherry, and M. Kharrazi The spectrum of CFTR variants in nonwhite CF patients: implications for molecular diagnostic testing J Mol Diagn 18 2016 39 50
28. L. Mamanova, A.J. Coffey, C.E. Scott, I. Kozarewa, E.H. Turner, A. Kumar, E. Howard, J. Shendure, and D.J. Turner Target-enrichment strategies for next-generation sequencing Nat Methods 7 2010 111 118
29. P. Shen, W. Wang, A.K. Chi, Y. Fan, R.W. Davis, and C. Scharfe Multiplex target capture with double-stranded DNA probes Genome Med 5 2013 50
30. C. Bombieri, M. Claustres, K. De Boeck, N. Derichs, J. Dodge, E. Girodon, I. Sermet, M. Schwarz, M. Tzetis, M. Wilschanski, C. Bareil, D. Bilton, C. Castellani, H. Cuppens, G.R. Cutting, P. Drevinek, P. Farrell, J.S. Elborn, K. Jarvi, B. Kerem, E. Kerem, M. Knowles, M. Macek Jr., A. Munck, D. Radojkovic, M. Seia, D.N. Sheppard, K.W. Southern, M. Stuhrmann, E. Tullis, J. Zielenski, P.F. Pignatti, and C. Ferec Recommendations for the classification of diseases as CFTR-related disorders J Cyst Fibros 10 Suppl 2 2011 S86 S102
31. A.M. Svensson, L.S. Chou, C.E. Miller, J.A. Robles, J.J. Swensen, K.V. Voelkerding, R. Mao, and E. Lyon Detection of large rearrangements in the cystic fibrosis transmembrane conductance regulator gene by multiplex ligation-dependent probe amplification assay when sequencing fails to detect two disease-causing mutations Genet Test Mol Biomarkers 14 2010 171 174
32. J.P. Schouten, C.J. McElgunn, R. Waaijer, D. Zwijnenburg, F. Diepvens, and G. Pals Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification Nucleic Acids Res 30 2002 e57
33. I. Schrijver, K. Rappahahn, L. Pique, M. Kharrazi, and L.J. Wong Multiplex ligation-dependent probe amplification identification of whole exon and single nucleotide deletions in the CFTR gene of Hispanic individuals with cystic fibrosis J Mol Diagn 10 2008 368 375
34. Y. Feng, D. Chen, G.L. Wang, V.W. Zhang, and L.J. Wong Improved molecular diagnosis by the detection of exonic deletions with target gene capture and deep sequencing Genet Med 17 2015 99 107
35. H.J. Abel, and E.J. Duncavage Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches Cancer Genet 206 2013 432 440
36. F.M. Hantash, A. Milunsky, Z. Wang, B. Anderson, W. Sun, A. Anguiano, and C.M. Strom A large deletion in the CFTR gene in CBAVD Genet Med 8 2006 93 95
37. J. Bonini, J. Varilh, C. Raynal, C. Theze, E. Beyne, M.P. Audrezet, C. Ferec, T. Bienvenu, E. Girodon, S. Tuffery-Giraud, M. Des Georges, M. Claustres, and M. Taulan-Cadars Small-scale high-throughput sequencing-based identification of new therapeutic tools in cystic fibrosis Genet Med 17 2015 796 806
38. T.J. Pugh, A.D. Delaney, N. Farnoud, S. Flibotte, M. Griffith, H.I. Li, H. Qian, P. Farinha, R.D. Gascoyne, and M.A. Marra Impact of whole genome amplification on analysis of copy number variants Nucleic Acids Res 36 2008 e80
39. F.M. Hantash, J.B. Redman, K. Starn, B. Anderson, A. Buller, M.J. McGinniss, F. Quan, M. Peng, W. Sun, and C.M. Strom Novel and recurrent rearrangements in the CFTR gene: clinical and laboratory implications for cystic fibrosis screening Hum Genet 119 2006 126 136
40. M.P. Audrezet, J.M. Chen, O. Raguenes, N. Chuzhanova, K. Giteau, C. Le Marechal, I. Quere, D.N. Cooper, and C. Ferec Genomic rearrangements in the CFTR gene: extensive allelic heterogeneity and diverse mutational mechanisms Hum Mutat 23 2004 343 357
41. T. Dork, M. Macek Jr., F. Mekus, B. Tummler, J. Tzountzouris, T. Casals, A. Krebsova, M. Koudova, I. Sakmaryova, M. Macek Sr., V. Vavrova, D. Zemkova, E. Ginter, N.V. Petrova, T. Ivaschenko, V. Baranov, M. Witt, A. Pogorzelski, J. Bal, C. Zekanowsky, K. Wagner, M. Stuhrmann, I. Bauer, H.H. Seydewitz, T. Neumann, and S. Jakubiczka Characterization of a novel 21-kb deletion, CFTRdele2,3(21 kb), in the CFTR gene: a cystic fibrosis mutation of Slavic origin common in Central and East Europe Hum Genet 106 2000 259 268
42. Y.L. Loukas, G. Thodi, E. Molou, V. Georgiou, Y. Dotsikas, and K.H. Schulpis Clinical diagnostic next-generation sequencing: the case of CFTR carrier screening Scand J Clin Lab Invest 75 2015 374 381