메뉴 건너뛰기




Volumn 18, Issue 9, 2016, Pages 940-948

Low-pass whole-genome sequencing in clinical cytogenetics: A validated approach

Author keywords

molecular karyotyping; next generation sequencing; pathogenic copy number variants

Indexed keywords

ABORTION; ADOLESCENT; ADULT; ANEUPLOIDY; ARTICLE; CHILD; CHROMOSOME ABERRATION; CHROMOSOME ANALYSIS; COPY NUMBER VARIATION; CYTOGENETICS; DIAGNOSTIC VALUE; FEASIBILITY STUDY; FEMALE; GENE TECHNOLOGY; GENOME; HUMAN; INFANT; MAJOR CLINICAL STUDY; MEDICAL GENETICS; MOSAICISM; MULTICENTER STUDY; NEWBORN; NEXT GENERATION SEQUENCING; PERINATAL PERIOD; PIPELINE; PRACTICE GUIDELINE; PRENATAL PERIOD; STILLBIRTH; VALIDATION STUDY; CHROMOSOME DISORDER; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; MALE; MICROARRAY ANALYSIS; PATHOLOGY; PRENATAL DIAGNOSIS; PROCEDURES; SPONTANEOUS ABORTION;

EID: 84985021248     PISSN: 10983600     EISSN: 15300366     Source Type: Journal    
DOI: 10.1038/gim.2015.199     Document Type: Article
Times cited : (137)

References (40)
  • 1
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • Abecasis GR, Auton A, Brooks LD, et al. An integrated map of genetic variation from 1,092 human genomes. Nature 2012; 491: 56-65
    • (2012) Nature , vol.491 , pp. 56-65
    • Abecasis, G.R.1    Auton, A.2    Brooks, L.D.3
  • 2
    • 62549085618 scopus 로고    scopus 로고
    • Human genetic variation, and its contribution to complex traits
    • Frazer KA, Murray SS, Schork NJ, Topol EJ. Human genetic variation, and its contribution to complex traits. Nat Rev Genet 2009; 10: 241-251
    • (2009) Nat Rev Genet , vol.10 , pp. 241-251
    • Frazer, K.A.1    Murray, S.S.2    Schork, N.J.3    Topol, E.J.4
  • 3
    • 84893733661 scopus 로고    scopus 로고
    • The 22q11.2 deletion syndrome as a window into complex neuropsychiatric disorders over the lifespan
    • Jonas RK, Montojo CA, Bearden CE. The 22q11.2 deletion syndrome as a window into complex neuropsychiatric disorders over the lifespan. Biol Psychiatry 2014; 75: 351-360
    • (2014) Biol Psychiatry , vol.75 , pp. 351-360
    • Jonas, R.K.1    Montojo, C.A.2    Bearden, C.E.3
  • 4
    • 77649083119 scopus 로고    scopus 로고
    • The angelman syndrome protein ube3a regulates synapse development by ubiquitinating arc
    • Greer PL, Hanayama R, Bloodgood BL, et al. The Angelman Syndrome protein Ube3A regulates synapse development by ubiquitinating arc. Cell 2010; 140: 704-716
    • (2010) Cell , vol.140 , pp. 704-716
    • Greer, P.L.1    Hanayama, R.2    Bloodgood, B.L.3
  • 5
    • 0027494343 scopus 로고
    • De novo truncation of chromosome 16p and healing with (TTAGGG)n in the alphathalassemia/mental retardation syndrome (ATR-16
    • Lamb J, Harris PC, Wilkie AO, Wood WG, Dauwerse JG, Higgs DR. De novo truncation of chromosome 16p, and healing with (TTAGGG)n in the alphathalassemia/mental retardation syndrome (ATR-16). Am J Hum Genet 1993; 52: 668-676
    • (1993) Am J Hum Genet , vol.52 , pp. 668-676
    • Lamb, J.1    Harris, P.C.2    Wilkie, A.O.3    Wood, W.G.4    Dauwerse, J.G.5    Higgs, D.R.6
  • 6
    • 84873314664 scopus 로고    scopus 로고
    • Gene copy-number alterations: A cost-benefit analysis
    • Tang YC, Amon A. Gene copy-number alterations: a cost-benefit analysis. Cell 2013; 152: 394-405
    • (2013) Cell , vol.152 , pp. 394-405
    • Tang, Y.C.1    Amon, A.2
  • 7
    • 81155160840 scopus 로고    scopus 로고
    • Identification of submicroscopic chromosomal aberrations in fetuses with increased nuchal translucency, and apparently normal karyotype
    • Leung TY, Vogel I, Lau TK, et al. Identification of submicroscopic chromosomal aberrations in fetuses with increased nuchal translucency, and apparently normal karyotype. Ultrasound Obstet Gynecol 2011; 38: 314-319
    • (2011) Ultrasound Obstet Gynecol , vol.38 , pp. 314-319
    • Leung, T.Y.1    Vogel, I.2    Lau, T.K.3
  • 8
    • 79958162661 scopus 로고    scopus 로고
    • Comprehensive assessment of array-based platforms, and calling algorithms for detection of copy number variants
    • Pinto D, Darvishi K, Shi X, et al. Comprehensive assessment of array-based platforms, and calling algorithms for detection of copy number variants. Nat Biotechnol 2011; 29: 512-520
    • (2011) Nat Biotechnol , vol.29 , pp. 512-520
    • Pinto, D.1    Darvishi, K.2    Shi, X.3
  • 9
    • 18144425478 scopus 로고    scopus 로고
    • A genome-wide scalable SNP genotyping assay using microarray technology
    • Gunderson KL, Steemers FJ, Lee G, Mendoza LG, Chee MS. A genome-wide scalable SNP genotyping assay using microarray technology. Nat Genet 2005; 37: 549-554
    • (2005) Nat Genet , vol.37 , pp. 549-554
    • Gunderson, K.L.1    Steemers, F.J.2    Lee, G.3    Mendoza, L.G.4    Chee, M.S.5
  • 10
    • 84975804424 scopus 로고    scopus 로고
    • 1000 genomes project mapping copy number variation by population-scale genome sequencing
    • Mills RE, Walter K, Stewart C, et al. 1000 Genomes Project. Mapping copy number variation by population-scale genome sequencing. Nature 2011; 470: 59-65
    • (2011) Nature , vol.470 , pp. 59-65
    • Mills, R.E.1    Walter, K.2    Stewart, C.3
  • 11
    • 84942876400 scopus 로고    scopus 로고
    • Traditional karyotyping vs copy number variation sequencing for detection of chromosomal abnormalities associated with spontaneous miscarriage
    • Lui S, Song L, Cram DS, et al. Traditional karyotyping vs copy number variation sequencing for detection of chromosomal abnormalities associated with spontaneous miscarriage. Ultrasound Obstet Gynecol 2015; 46: 472-477
    • (2015) Ultrasound Obstet Gynecol , vol.46 , pp. 472-477
    • Lui, S.1    Song, L.2    Cram, D.S.3
  • 12
    • 84906281405 scopus 로고    scopus 로고
    • Copy number variation sequencing for comprehensive diagnosis of chromosome disease syndromes
    • Liang D, Peng Y, Lv W, et al. Copy number variation sequencing for comprehensive diagnosis of chromosome disease syndromes. J Mol Diagn 2014; 16: 519-526
    • (2014) J Mol Diagn , vol.16 , pp. 519-526
    • Liang, D.1    Peng, Y.2    Lv, W.3
  • 13
    • 84902336049 scopus 로고    scopus 로고
    • PSCC: Sensitive, and reliable population-scale copy number variation detection method based on low coverage sequencing
    • Li X, Chen S, Xie W, et al. PSCC: sensitive, and reliable population-scale copy number variation detection method based on low coverage sequencing. PLoS One 2014; 9: e85096
    • (2014) Plos One , vol.9 , pp. e85096
    • Li, X.1    Chen, S.2    Xie, W.3
  • 14
    • 84875185177 scopus 로고    scopus 로고
    • Comparative studies of copy number variation detection methods for next-generation sequencing technologies
    • Duan J, Zhang JG, Deng HW, Wang YP. Comparative studies of copy number variation detection methods for next-generation sequencing technologies. PLoS One 2013; 8: e59128
    • (2013) Plos One , vol.8 , pp. e59128
    • Duan, J.1    Zhang, J.G.2    Deng, H.W.3    Wang, Y.P.4
  • 15
    • 55549097849 scopus 로고    scopus 로고
    • The diploid genome sequence of an Asian individual
    • Wang J, Wang W, Li R, et al. The diploid genome sequence of an Asian individual. Nature 2008; 456: 60-65
    • (2008) Nature , vol.456 , pp. 60-65
    • Wang, J.1    Wang, W.2    Li, R.3
  • 16
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: An improved ultrafast tool for short read alignment
    • Li R, Yu C, Li Y, et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009; 25: 1966-1967
    • (2009) Bioinformatics , vol.25 , pp. 1966-1967
    • Li, R.1    Yu, C.2    Li, Y.3
  • 17
    • 84874544894 scopus 로고    scopus 로고
    • Rapid detection of aneuploidies on a benchtop sequencing platform
    • Xie W, Tan Y, Li X, et al. Rapid detection of aneuploidies on a benchtop sequencing platform. Prenat Diagn 2013; 33: 232-237
    • (2013) Prenat Diagn , vol.33 , pp. 232-237
    • Xie, W.1    Tan, Y.2    Li, X.3
  • 18
    • 84873664159 scopus 로고    scopus 로고
    • Improving detection of copy-number variation by simultaneous bias correction, and read-depth segmentation
    • Szatkiewicz JP, Wang W, Sullivan PF, Wang W, Sun W. Improving detection of copy-number variation by simultaneous bias correction, and read-depth segmentation. Nucleic Acids Res 2013; 41: 1519-1532
    • (2013) Nucleic Acids Res , vol.41 , pp. 1519-1532
    • Szatkiewicz, J.P.1    Wang, W.2    Sullivan, P.F.3    Wang, W.4    Sun, W.5
  • 19
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads, and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads, and calling variants using mapping quality scores. Genome Res 2008; 18: 1851-1858
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 20
    • 79960812993 scopus 로고    scopus 로고
    • American college of medical genetics standards, and guidelines for interpretation, and reporting of postnatal constitutional copy number variants
    • Working Group of the American College of Medical Genetics Laboratory Quality Assurance Committee
    • Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST; Working Group of the American College of Medical Genetics Laboratory Quality Assurance Committee. American College of Medical Genetics standards, and guidelines for interpretation, and reporting of postnatal constitutional copy number variants. Genet Med 2011; 13: 680-685
    • (2011) Genet Med , vol.13 , pp. 680-685
    • Kearney, H.M.1    Thorland, E.C.2    Brown, K.K.3    Quintero-Rivera, F.4    South, S.T.5
  • 21
    • 84938932937 scopus 로고    scopus 로고
    • A novel 11p13 microdeletion encompassing PAX6 in a Chinese Han family with aniridia, ptosis, and mental retardation
    • Hu P, Meng L, Ma D, et al. A novel 11p13 microdeletion encompassing PAX6 in a Chinese Han family with aniridia, ptosis, and mental retardation. Mol Cytogenet 2015; 8: 3
    • (2015) Mol Cytogenet , vol.8 , pp. 3
    • Hu, P.1    Meng, L.2    Ma, D.3
  • 22
    • 79952118382 scopus 로고    scopus 로고
    • Multiplex ligation-dependent probe amplification (MLPA®) for the detection of copy number variation in genomic sequences
    • Eijk-Van Os PG, Schouten JP. Multiplex ligation-dependent probe amplification (MLPA®) for the detection of copy number variation in genomic sequences. Methods Mol Biol 2011; 688: 97-126
    • (2011) Methods Mol Biol , vol.688 , pp. 97-126
    • Eijk-Van Os, P.G.1    Schouten, J.P.2
  • 23
    • 84898775166 scopus 로고    scopus 로고
    • A robust approach for blind detection of balanced chromosomal rearrangements with whole-genome low-coverage sequencing
    • Dong Z, Jiang L, Yang C, et al. A robust approach for blind detection of balanced chromosomal rearrangements with whole-genome low-coverage sequencing. Hum Mutat 2014; 35: 625-636
    • (2014) Hum Mutat , vol.35 , pp. 625-636
    • Dong, Z.1    Jiang, L.2    Yang, C.3
  • 24
    • 64249126720 scopus 로고    scopus 로고
    • Haplotype-sharing analysis implicates chromosome 7q36 harboring DPP6 in familial idiopathic ventricular fibrillation
    • Alders M, Koopmann TT, Christiaans I, et al. Haplotype-sharing analysis implicates chromosome 7q36 harboring DPP6 in familial idiopathic ventricular fibrillation. Am J Hum Genet 2009; 84: 468-476
    • (2009) Am J Hum Genet , vol.84 , pp. 468-476
    • Alders, M.1    Koopmann, T.T.2    Christiaans, I.3
  • 25
    • 82555194123 scopus 로고    scopus 로고
    • Two-marker association tests yield new disease associations for coronary artery disease, and hypertension
    • Slavin TP, Feng T, Schnell A, Zhu X, Elston RC. Two-marker association tests yield new disease associations for coronary artery disease, and hypertension. Hum Genet 2011; 130: 725-733
    • (2011) Hum Genet , vol.130 , pp. 725-733
    • Slavin, T.P.1    Feng, T.2    Schnell, A.3    Zhu, X.4    Elston, R.C.5
  • 26
    • 84872168658 scopus 로고    scopus 로고
    • The detection of mosaicism by prenatal BoBs™
    • Cheng YK, Wong C, Wong HK, et al. The detection of mosaicism by prenatal BoBs™. Prenat Diagn 2013; 33: 42-49
    • (2013) Prenat Diagn , vol.33 , pp. 42-49
    • Cheng, Y.K.1    Wong, C.2    Wong, H.K.3
  • 27
    • 0042828948 scopus 로고    scopus 로고
    • Molecular characterisation of the 22q13 deletion syndrome supports the role of haploinsufficiency of SHANK3/PROSAP2 in the major neurological symptoms
    • Wilson HL, Wong AC, Shaw SR, et al. Molecular characterisation of the 22q13 deletion syndrome supports the role of haploinsufficiency of SHANK3/PROSAP2 in the major neurological symptoms. J Med Genet 2003; 40: 575-584
    • (2003) J Med Genet , vol.40 , pp. 575-584
    • Wilson, H.L.1    Wong, A.C.2    Shaw, S.R.3
  • 28
    • 84884527350 scopus 로고    scopus 로고
    • A PARK2 polymorphism associated with delayed neuropsychological sequelae after carbon monoxide poisoning
    • Liang F, Li W, Zhang P, et al. A PARK2 polymorphism associated with delayed neuropsychological sequelae after carbon monoxide poisoning. BMC Med Genet 2013; 14: 99
    • (2013) BMC Med Genet , vol.14 , pp. 99
    • Liang, F.1    Li, W.2    Zhang, P.3
  • 29
    • 84870567269 scopus 로고    scopus 로고
    • Nichd stillbirth collaborative research network karyotype versus microarray testing for genetic abnormalities after stillbirth
    • Reddy UM, Page GP, Saade GR, et al. NICHD Stillbirth Collaborative Research Network. Karyotype versus microarray testing for genetic abnormalities after stillbirth. N Engl J Med 2012; 367: 2185-2193
    • (2012) N Engl J Med , vol.367 , pp. 2185-2193
    • Reddy, U.M.1    Page, G.P.2    Saade, G.R.3
  • 30
    • 84919691734 scopus 로고    scopus 로고
    • Molecular, and cytogenetic analysis in stillbirth: Results from 481 consecutive cases
    • Sahlin E, Gustavsson P, Liedén A, et al. Molecular, and cytogenetic analysis in stillbirth: results from 481 consecutive cases. Fetal Diagn Ther 2014; 36: 326-332
    • (2014) Fetal Diagn Ther , vol.36 , pp. 326-332
    • Sahlin, E.1    Gustavsson, P.2    Liedén, A.3
  • 31
    • 84902546412 scopus 로고    scopus 로고
    • Performance of chromosomal microarray for patients with intellectual disabilities/developmental delay, autism, and multiple congenital anomalies in a Chinese cohort
    • Chong WW, Lo IF, Lam ST, et al. Performance of chromosomal microarray for patients with intellectual disabilities/developmental delay, autism, and multiple congenital anomalies in a Chinese cohort. Mol Cytogenet 2014; 7: 34
    • (2014) Mol Cytogenet , vol.7 , pp. 34
    • Chong, W.W.1    Lo, I.F.2    Lam, S.T.3
  • 32
    • 62149085882 scopus 로고    scopus 로고
    • Detection of cryptic pathogenic copy number variations, and constitutional loss of heterozygosity using high resolution SNP microarray analysis in 117 patients referred for cytogenetic analysis, and impact on clinical practice
    • Bruno DL, Ganesamoorthy D, Schoumans J, et al. Detection of cryptic pathogenic copy number variations, and constitutional loss of heterozygosity using high resolution SNP microarray analysis in 117 patients referred for cytogenetic analysis, and impact on clinical practice. J Med Genet 2009; 46: 123-131
    • (2009) J Med Genet , vol.46 , pp. 123-131
    • Bruno, D.L.1    Ganesamoorthy, D.2    Schoumans, J.3
  • 33
    • 84885942337 scopus 로고    scopus 로고
    • Application of microarray-based comparative genomic hybridization in prenatal, and postnatal settings: Three case reports
    • Liu J, Bernier F, Lauzon J, Lowry RB, Chernos J. Application of microarray-based comparative genomic hybridization in prenatal, and postnatal settings: three case reports. Genet Res Int 2011; 2011: 976398
    • (2011) Genet Res Int , vol.2011 , pp. 976398
    • Liu, J.1    Bernier, F.2    Lauzon, J.3    Lowry, R.B.4    Chernos, J.5
  • 34
    • 84863279486 scopus 로고    scopus 로고
    • Informatics enhanced SNP microarray analysis of 30 miscarriage samples compared to routine cytogenetics
    • Lathi RB, Massie JA, Loring M, et al. Informatics enhanced SNP microarray analysis of 30 miscarriage samples compared to routine cytogenetics. PLoS One 2012; 7: e31282
    • (2012) Plos One , vol.7 , pp. e31282
    • Lathi, R.B.1    Massie, J.A.2    Loring, M.3
  • 35
    • 84870549609 scopus 로고    scopus 로고
    • Chromosomal microarray versus karyotyping for prenatal diagnosis
    • Wapner RJ, Martin CL, Levy B, et al. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med 2012; 367: 2175-2184
    • (2012) N Engl J Med , vol.367 , pp. 2175-2184
    • Wapner, R.J.1    Martin, C.L.2    Levy, B.3
  • 36
    • 39749154724 scopus 로고    scopus 로고
    • A recurrent 15q13.3 microdeletion syndrome associated with mental retardation, and seizures
    • Sharp AJ, Mefford HC, Li K, et al. A recurrent 15q13.3 microdeletion syndrome associated with mental retardation, and seizures. Nat Genet 2008; 40: 322-328
    • (2008) Nat Genet , vol.40 , pp. 322-328
    • Sharp, A.J.1    Mefford, H.C.2    Li, K.3
  • 37
    • 84886811866 scopus 로고    scopus 로고
    • Computational tools for copy number variation (CNV) detection using next-generation sequencing data: Features, and perspectives
    • Zhao M, Wang Q, Wang Q, Jia P, Zhao Z. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features, and perspectives. BMC Bioinformatics 2013; 14(suppl 11): S1
    • (2013) BMC Bioinformatics , vol.14 , pp. S1
    • Zhao, M.1    Wang, Q.2    Wang, Q.3    Jia, P.4    Zhao, Z.5
  • 38
    • 33745906844 scopus 로고    scopus 로고
    • Phenotype of triploid embryos
    • McFadden DE, Robinson WP. Phenotype of triploid embryos. J Med Genet 2006; 43: 609-612
    • (2006) J Med Genet , vol.43 , pp. 609-612
    • McFadden, D.E.1    Robinson, W.P.2
  • 39
    • 84940737616 scopus 로고    scopus 로고
    • Current knowledge of prenatal diagnosis of mosaic autosomal trisomy in amniocytes: Karyotype/phenotype correlations
    • Wallerstein R, Misra S, Dugar RB, Alem M, Mazzoni R, Garabedian MJ. Current knowledge of prenatal diagnosis of mosaic autosomal trisomy in amniocytes: karyotype/phenotype correlations. Prenat Diagn 2015; 35: 841-847
    • (2015) Prenat Diagn , vol.35 , pp. 841-847
    • Wallerstein, R.1    Misra, S.2    Dugar, R.B.3    Alem, M.4    Mazzoni, R.5    Garabedian, M.J.6
  • 40
    • 84872155951 scopus 로고    scopus 로고
    • Application of a new molecular technique for the genetic evaluation of products of conception
    • Grati FR, Gomes DM, Ganesamoorthy D, et al. Application of a new molecular technique for the genetic evaluation of products of conception. Prenat Diagn 2013; 33: 32-41
    • (2013) Prenat Diagn , vol.33 , pp. 32-41
    • Grati, F.R.1    Gomes, D.M.2    Ganesamoorthy, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.