Oligonucleotide Microarrays for Clinical Diagnosis of Copy Number Variation

Abstract

Detection of genomic copy number variation is now considered the standard of care in the evaluation of children with developmental delay, and is used for other clinical indications such as multiple congenital anomalies and autism spectrum disorders. Fluorescence in situ hybridization (FISH) was the first molecular method for detection of submicroscopic genomic copy number variation, but microarray based comparative genomic hybridization (array CGH) offers several advantages as an adjunct to traditional cytogenetic methods such as karyotype and FISH. This unit focuses on oligonucleotide arrays, but includes background information on basic differences between oligonucleotide arrays and bacterial artificial chromosome (BAC) arrays. Array sensitivity is influenced by probe coverage or density, probe location, and choice of oligo array formats (i.e., targeted versus whole genome). Array platform influences the likelihood of detecting variants of unknown significance. Clinical interpretation of such variants is discussed.

Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities

“…For example, many clinicians are unaware that a whole genome oligoarray can detect clinically significant copy number changes missed on a targeted BAC array30 or that a SNP array can detect long contiguous stretches of homozygosity that can be associated with uniparental disomy or consanguinity, both of which increase the risk for autosomal recessive conditions.…”

“…Although microarray analysis is proficient in characterizing chromosomal imbalances (which ultimately improves patient care), 29 clinicians ordering the test need to be aware of the different clinical platforms (e.g., BAC versus oligo, targeted versus whole genome, and SNP), the variation in resolution among arrays and the information each provides. For example, many clinicians are unaware that a whole genome oligoarray can detect clinically significant copy number changes missed on a targeted BAC array 30 or that a SNP array can detect long contiguous stretches of homozygosity that can be associated with uniparental disomy or consanguinity, both of which increase the risk for autosomal recessive conditions.…”

Translocations Disrupting PHF21A in the Potocki-Shaffer-Syndrome Region Are Associated with Intellectual Disability and Craniofacial Anomalies

“…7,15,18 Where possible, all subjects were tested for copynumber variants (CNVs) by array comparative genomic hybridization (CGH) with the use of Agilent (Santa Clara, CA) 244K arrays as described (Table 2). 19 DGAP012 displayed one 156 kb deletion CNV (chr13: 48,430,969-48,587,500; hg18) that is located at 13q14.2 and has not been reported previously and that involves FNDC3A, which is expressed in spermatids and Leydig cells and produces male sterility when homozygously inactivated. 20 All human studies were performed under informed-consent protocols approved by the Partners HealthCare System Human Research Committee.…”

“…(C) FISH analysis with a 30 kb SnaBI restriction fragment (signal shown in green) from BAC CTD-3193O13, which has previously been reported as a breakpoint-crossing clone. 24 Probe hybridization is seen on the normal 19, der (19), and der(11) chromosomes, indicating that this 30 kb restriction fragment spans the chromosome 19 breakpoint region (Figure S1B). (D) FISH analysis with 37 kb fosmid G248P88722D5 spanning the breakpoints on the normal 11, der(1), and der(11) chromosomes, indicating that the translocation breakpoint of the chromosome 11 is located within the sequence of this genomic clone.…”

“…The der (19) junction fragment was amplified by nested PCR with the following primer pairs: chr11 forward 1 þ chr19 reverse 1 for boost PCR and chr11 forward 2 þ chr19 reverse 2 for nested PCR. The der(11) junction fragment was amplified by nested PCR with the following primer pairs: chr19 forward 1 þ chr11 reverse 1 for boost PCR and chr19 forward 2 þ chr11 reverse 2 for nested PCR (Table S3).…”