Validation of a high resolution NGS method for detecting spinal muscular atrophy carriers among phase 3 participants in the 1000 Genomes Project

BMC Medical Genetics

Volumn 16, Issue 1, 2015, Pages

  Larson, Jessica L ^a   Silver, Ari J ^a   Chan, Dalin ^a   Borroto, Carlos ^a   Spurrier, Brett ^a   Silver, Lee M ^a,b  

^a GenePeeks Inc   (United States)

^b PRINCETON UNIVERSITY   (United States)

Author keywords

1000 Genomes Project; Carrier testing; DNA seq; Exome seq; Genetic testing; Next generation sequencing (NGS); SMN1; SMN2; Spinal muscular atrophy (SMA)

Indexed keywords

GENOMIC DNA; SURVIVAL MOTOR NEURON PROTEIN 1; SURVIVAL MOTOR NEURON PROTEIN 2; SMN1 PROTEIN, HUMAN; SMN2 PROTEIN, HUMAN;

ADULT; ARTICLE; BAYES THEOREM; COHORT ANALYSIS; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA SEQUENCE; EXOME; GENE FREQUENCY; GENE LOCUS; GENETIC PREDISPOSITION; GENETIC SCREENING; HETEROZYGOTE DETECTION; HUMAN; MAJOR CLINICAL STUDY; MALE; MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION; NEXT GENERATION SEQUENCING; POLYMERASE CHAIN REACTION; POPULATION GENETICS; SMN1 GENE; SMN2 GENE; SPINAL MUSCULAR ATROPHY; VALIDATION PROCESS; BIOLOGICAL MODEL; CASE CONTROL STUDY; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME PROJECT; MULTIPLEX POLYMERASE CHAIN REACTION; PROCEDURES; VALIDATION STUDY;

CASE-CONTROL STUDIES; COHORT STUDIES; HETEROZYGOTE DETECTION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMAN GENOME PROJECT; HUMANS; MODELS, GENETIC; MULTIPLEX POLYMERASE CHAIN REACTION; MUSCULAR ATROPHY, SPINAL; SURVIVAL OF MOTOR NEURON 1 PROTEIN; SURVIVAL OF MOTOR NEURON 2 PROTEIN;

EID: 84945952079     PISSN: None     EISSN: 14712350     Source Type: Journal    
DOI: 10.1186/s12881-015-0246-2     Document Type: Article

References (41)

1. Pearn J. Classification of spinal muscular atrophies. Lancet. 1980;1:919-22.
2. Lunn MR, Wang CH. Spinal muscular atrophy. Lancet. 2008;371:2120-33.
3. Munsat TL, Davies KE. International SMA consortium meeting. (26-28 June 1992, Bonn, Germany). Neuromuscul Disord. 1992;2:423-8.
4. D'Amico A, Mercuri E, Tiziano FD, Bertini E. Spinal muscular atrophy. Orphanet J Rare Dis. 2011;6:71.
5. Rochette CF, Gilbert N, Simard LR. SMN gene duplication and the emergence of the SMN2 gene occurred in distinct hominids: SMN2 is unique to Homo sapiens. Hum Genet. 2001;108:255-66.
6. Lefebvre S, Bürglen L, Reboullet S, Clermont O, Burlet P, Viollet L, et al. Identification and characterization of a spinal muscular atrophy-determining gene. Cell. 1995;80:155-65.
7. Bürglen L, Lefebvre S, Clermont O, Burlet P, Viollet L, Cruaud C, et al. Structure and organization of the human survival motor neurone (SMN) gene. Genomics. 1996;32:479-82.
8. Melki J, Lefebvre S, Bürglen L, Burlet P, Clermont O, Millasseau P, et al. De novo and inherited deletions of the 5q13 region in spinal muscular atrophies. Science. 1994;264:1474-7.
9. Monani UR, Lorson CL, Parsons DW, Prior TW, Androphy EJ, Burghes AH, et al. A single nucleotide difference that alters splicing patterns distinguishes the SMA gene SMN1 from the copy gene SMN2. Hum Mol Genet. 1999;8:1177-83.
10. Prior TW, Snyder PJ, Rink BD, Pearl DK, Pyatt RE, Mihal DC, et al. Newborn and carrier screening for spinal muscular atrophy. Am J Med Genet A. 2010;152A:1608-16.
11. Lefebvre S, Burlet P, Liu Q, Bertrandy S, Clermont O, Munnich A, et al. Correlation between severity and SMN protein level in spinal muscular atrophy. Nat Genet. 1997;16:265-9.
12. Martínez-Hernández R, Bernal S, Also-Rallo E, Alías L, Barceló MJ, Hereu M, et al. Synaptic defects in type I spinal muscular atrophy in human development. J Pathol. 2013;229:49-61.
13. Soler-Botija C, Cuscó I, Caselles L, López E, Baiget M, Tizzano EF. Implication of fetal SMN2 expression in type I SMA pathogenesis: protection or pathological gain of function? J Neuropathol Exp Neurol. 2005;64:215-23.
14. MacDonald WK, Hamilton D, Kuhle S. SMA carrier testing: a meta-analysis of differences in test performance by ethnic group. Prenat Diagn. 2014;34:1219-26.
15. Prior TW, Nagan N, Sugarman EA, Batish SD, Braastad C. Technical standards and guidelines for spinal muscular atrophy testing. Genet Med. 2011;13:686-94.
16. Ogino S, Wilson RB, Gold B. New insights on the evolution of the SMN1 and SMN2 region: simulation and meta-analysis for allele and haplotype frequency calculations. Eur J Hum Genet. 2004;12:1015-23.
17. Ogino S, Gao S, Leonard DGB, Paessler M, Wilson RB. Inverse correlation between SMN1 and SMN2 copy numbers: evidence for gene conversion from SMN2 to SMN1. Eur J Hum Genet. 2003;11:275-7.
18. Ogino S, Leonard DGB, Rennert H, Ewens WJ, Wilson RB. Genetic risk assessment in carrier testing for spinal muscular atrophy. Am J Med Genet. 2002;110:301-7.
19. Sugarman EA, Nagan N, Zhu H, Akmaev VR, Zhou Z, Rohlfs EM, et al. Pan-ethnic carrier screening and prenatal diagnosis for spinal muscular atrophy: clinical laboratory analysis of >72,400 specimens. Eur J Hum Genet. 2012;20:27-32.
20. Wirth B. An update of the mutation spectrum of the survival motor neuron gene (SMN1) in autosomal recessive spinal muscular atrophy (SMA). Hum Mutat. 2000;15:228-37.
21. Prior TW. Carrier screening for spinal muscular atrophy. Genet Med. 2008;10:840-2.
22. Feldkötter M, Schwarzer V, Wirth R, Wienker TF, Wirth B. Quantitative analyses of SMN1 and SMN2 based on real-time lightCycler PCR: fast and highly reliable carrier testing and prediction of severity of spinal muscular atrophy. Am J Hum Genet. 2002;70:358-68.
23. Huang C-H, Chang Y-Y, Chen C-H, Kuo Y-S, Hwu W-L, Gerdes T, et al. Copy number analysis of survival motor neuron genes by multiplex ligation-dependent probe amplification. Genet Med. 2007;9:241-8.
24. Anhuf D, Eggermann T, Rudnik-Schöneborn S, Zerres K. Determination of SMN1 and SMN2 copy number using TaqMan technology. Hum Mutat. 2003;22:74-8.
25. van der Steege G, Grootscholten PM, van der Vlies P, Draaijers TG, Osinga J, Cobben JM, et al. PCR-based DNA test to confirm clinical diagnosis of autosomal recessive spinal muscular atrophy. Lancet. 1995;345:985-6.
26. Sutomo R, Akutsu T, Takeshima Y, Nishio H, Sadewa AH, Harada Y, et al. Rapid SMN1 deletion test using DHPLC to screen patients with spinal muscular atrophy. Am J Med Genet. 2002;113:225-6.
27. Kubo Y, Nishio H, Saito K. A new method for SMN1 and hybrid SMN gene analysis in spinal muscular atrophy using long-range PCR followed by sequencing. J Hum Genet. 2015;60:233-9.
28. Nurputra DK, Lai PS, Harahap NIF, Morikawa S, Yamamoto T, Nishimura N, et al. Spinal muscular atrophy: from gene discovery to clinical trials. Ann Hum Genet. 2013;77:435-63.
29. Tomaszewicz K, Kang P, Wu B-L. Detection of homozygous and heterozygous SMN deletions of spinal muscular atrophy in a single assay with multiplex ligation-dependent probe amplification. Beijing Da Xue Xue Bao. 2005;37:55-7.
30. Scarciolla O, Stuppia L, De Angelis MV, Murru S, Palka C, Giuliani R, et al. Spinal muscular atrophy genotyping by gene dosage using multiple ligation-dependent probe amplification. Neurogenetics. 2006;7:269-76.
31. Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, Ganusova EE, Mudge J, et al. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med. 2011;3:65ra4.
32. McVean GA, Altshuler Co-Chair DM, Durbin Co-Chair RM, Abecasis GR, Bentley DR, Chakravarti A, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491:56-65.
33. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589-95.
34. Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, del Angel G, Levy-Moonshine A, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;11:11.10.1-11.10.33.
35. Peeters K, Chamova T, Jordanova A. Clinical and genetic diversity of SMN1-negative proximal spinal muscular atrophies. Brain. 2014;137:2879-96.
36. Alías L, Barceló MJ, Bernal S, Martínez-Hernández R, Also-Rallo E, Vázquez C, et al. Improving detection and genetic counseling in carriers of spinal muscular atrophy with two copies of the SMN1 gene. Clin Genet. 2014;85:470-5.
37. Mailman MD, Hemingway T, Darsey RL, Glasure CE, Huang Y, Chadwick RB, et al. Hybrids monosomal for human chromosome 5 reveal the presence of a spinal muscular atrophy (SMA) carrier with two SMN1 copies on one chromosome. Hum Genet. 2001;108:109-15.
38. Smith M, Calabro V, Chong B, Gardiner N, Cowie S, Sart du D. Population screening and cascade testing for carriers of SMA. Eur J Hum Genet. 2007;15:759-66.
39. Luo M, Liu L, Peter I, Zhu J, Scott SA, Zhao G, et al. An Ashkenazi Jewish SMN1 haplotype specific to duplication alleles improves pan-ethnic carrier screening for spinal muscular atrophy. Genet Med. 2014;16:149-56.
40. Wirth B, Schmidt T, Hahnen E, Rudnik-Schöneborn S, Krawczak M, Müller-Myhsok B, et al. De novo rearrangements found in 2 % of index patients with spinal muscular atrophy: mutational mechanisms, parental origin, mutation rate, and implications for genetic counseling. Am J Hum Genet. 1997;61:1102-11.
41. Rehm HL. Disease-targeted sequencing: a cornerstone in the clinic. Nat Rev Genet. 2013;14:295-300.