1
|
Wiszniewska J, Bi W, Shaw C, Stankiewicz P, Kang SHL, Pursley AN, Lalani S, Hixson P, Gambin T, Tsai CH, Bock HG, Descartes M, Probst FJ, Scaglia F, Beaudet AL, Lupski JR, Eng C, Cheung SW, Bacino C, Patel A. Combined array CGH plus SNP genome analyses in a single assay for optimized clinical testing. Eur J Hum Genet 2013; 22:79-87. [PMID: 23695279 PMCID: PMC3865406 DOI: 10.1038/ejhg.2013.77] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 01/28/2013] [Accepted: 03/12/2013] [Indexed: 02/06/2023] Open
Abstract
In clinical diagnostics, both array comparative genomic hybridization (array CGH) and single nucleotide polymorphism (SNP) genotyping have proven to be powerful genomic technologies utilized for the evaluation of developmental delay, multiple congenital anomalies, and neuropsychiatric disorders. Differences in the ability to resolve genomic changes between these arrays may constitute an implementation challenge for clinicians: which platform (SNP vs array CGH) might best detect the underlying genetic cause for the disease in the patient? While only SNP arrays enable the detection of copy number neutral regions of absence of heterozygosity (AOH), they have limited ability to detect single-exon copy number variants (CNVs) due to the distribution of SNPs across the genome. To provide comprehensive clinical testing for both CNVs and copy-neutral AOH, we enhanced our custom-designed high-resolution oligonucleotide array that has exon-targeted coverage of 1860 genes with 60 000 SNP probes, referred to as Chromosomal Microarray Analysis – Comprehensive (CMA-COMP). Of the 3240 cases evaluated by this array, clinically significant CNVs were detected in 445 cases including 21 cases with exonic events. In addition, 162 cases (5.0%) showed at least one AOH region >10 Mb. We demonstrate that even though this array has a lower density of SNP probes than other commercially available SNP arrays, it reliably detected AOH events >10 Mb as well as exonic CNVs beyond the detection limitations of SNP genotyping. Thus, combining SNP probes and exon-targeted array CGH into one platform provides clinically useful genetic screening in an efficient manner.
Collapse
Affiliation(s)
- Joanna Wiszniewska
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sung-Hae L Kang
- Allina Cytogenetics Laboratory, Abbott Northwestern Hospital, Minneapolis, MN, USA
| | - Amber N Pursley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Seema Lalani
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Patricia Hixson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Chun-hui Tsai
- 1] Department of Molecular and Medical Genetics, Oregon Health and Sciences University-OHSU, Portland, OR, USA [2] Department of Pediatrics, The Children's Hospital, University of Colorado School of Medicine, Aurora, CO, USA
| | - Hans-Georg Bock
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Maria Descartes
- Department of Genetics, University of Alabama, Birmingham, AL, USA
| | - Frank J Probst
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arthur L Beaudet
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Christine Eng
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sau Wai Cheung
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Carlos Bacino
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|