Microarrays

Melissa Stosic, Jessica L. Giordano, Brynn Levy, and Ronald Wapner

Introduction

Chromosomal microarray analysis (CMA) by which chromosomal anomalies beyond the resolution of traditional karyotyping can be identified has become a mainstay of prenatal diagnosis over the past several years. In 2012, a landmark study was published comparing CMA to the previous standard of care, karyotype analysis, which can identify aneuploidy and chromosomal structural changes bigger than 7–10 million base pairs (Mb) (1). It was shown that CMA was able to detect all of the unbalanced changes identified on karyotype as well as additional microdeletions and duplications (copy number changes [CNVs]) in 1.7% of pregnancies without ultrasound anomalies. In pregnancies with a structural anomaly and a normal karyotype, 6% of fetuses had a clinically significant CNV identified by CMA. This incremental yield of CMA over karyotype led the American College of Obstetricians and Gynecologists (ACOG) along with the Society for Maternal-Fetal Medicine (SMFM) to publish guidelines suggesting that microarray be the preferred test for anomalous pregnancies. They also commented that in average-risk pregnancies undergoing invasive testing for indications such as advanced maternal age or abnormal screening, either karyotype or CMA is appropriate (2).

Basics of chromosomal microarray analysis

Standard karyotype is able to detect CNVs that are 7–10 megabases (Mb), or million base pairs in size or greater, such as a monosomy, trisomy, or a large deletion or duplication. Fluorescence in situ hybridization (FISH) can identify smaller copy number changes in specific regions of the genome by utilizing probes specific to that region or chromosome. Comparatively, CMA has the ability to find microdeletions and duplications as small as 10 kilobases (kb) or thousand base pairs, across the entire genome. These small deletions and duplications are missed by standard karyotyping and can cause genetic syndromes with intellectual disabilities and/or structural abnormalities. Table 36.1 lists common microdeletion and microduplication syndromes and the major phenotypic features associated with each condition.

CMA is performed by mixing a control normal sample of fragmented DNA with DNA from the sample to be tested. Each sample is attached to a florescent dye of a different color (usually red and green). The mixture is then heated to denature (separate) the double-stranded DNA fragments from the patient and the control into single strands. The mixture is then hybridized to a slide embedded with short probes of known DNA sequences. If an equal number of strands from the control and the patient are present at a location on the chip, this will be represented by an equal amount of red and green fragments. The slide is then read by a laser that evaluates all the locations on the slide and interprets their color. Deletions and duplications will appear as too much or too little of one color since the matching strand is either missing or overrepresented. Oligonucleotide arrays are “comparative” in that they compare the sample to a reference genome and are hence described as comparative genomic hybridization arrays (aCGH). This is illustrated in Figure 36.1.

A second type of array is the SNP microarray that uses high-density oligonucleotide-based arrays in which target probes are chosen from DNA locations known to vary between individuals by a single base pair, i.e., single nucleotide polymorphisms (SNPs). Today, most CMAs utilized for prenatal diagnosis are hybrid arrays that contain both SNP probes and copy number probes. By including SNPs on the array, additional clinically useful information such as uniparental disomy (UPD), zygosity, maternal cell contamination, parent of origin, and consanguinity, may be extracted from the genotype plots generated from the SNPs. Consanguinity and UPD can be responsible for recessive genetic conditions in the SNP regions with long contiguous stretches of homozygosity (LCSH), and UPD can cause disease when it occurs on an imprinted chromosome. Examples of imprinting disorders include Russell–Silver syndrome, which is caused by UPD 7; Prader–Willi syndrome, which results from maternal UPD 15; and Beckwith-Wiedemann syndrome, which occurs from partial UPD 11. In addition, triploidy, which cannot be detected by aCGH, can easily be identified by SNP oligonucleotide microarray analysis (SOMA) by assessing the SNP allele patterns on the array. (The allele plots should show four distinct tracks for every autosome, see Figure 36.2.)

Stay updated, free articles. Join our Telegram channel

Join