Research Article SNP Microarray in FISH Negative Clinically Suspected 22q11.2 Microdeletion Syndrome Ashutosh Halder, Manish Jain, and Amanpreet Kaur Kalsi Reproductive Biology, AIIMS, New Delhi 110029, India Correspondence should be addressed to Ashutosh Halder; ashutoshhalder@gmail.com Received 28 December 2015; Revised 27 January 2016; Accepted 16 February 2016 Academic Editor: Albert Basson Copyright © 2016 Ashutosh Halder et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Te present study evaluated the role of SNP microarray in 101 cases of clinically suspected FISH negative (noninformative/normal) 22q11.2 microdeletion syndrome. SNP microarray was carried out using 300K HumanCytoSNP-12 BeadChip array or CytoScan 750K array. SNP microarray identifed 8 cases of 22q11.2 microdeletions and/or microduplications in addition to cases of chromosomal abnormalities and other pathogenic/likely pathogenic CNVs. Clinically suspected specifc deletions (22q11.2) were detectable in approximately 8% of cases by SNP microarray, mostly from FISH noninformative cases. Tis study also identifed several LOH/AOH loci with known and well-defned UPD (uniparental disomy) disorders. In conclusion, this study suggests more strict clinical criteria for FISH analysis. However, if clinical criteria are few or doubtful, in particular newborn/neonate in intensive care, SNP microarray should be the frst screening test to be ordered. FISH is ideal test for detecting mosaicism, screening family members, and prenatal diagnosis in proven families. 1. Introduction Te 22q11.2 microdeletion syndrome is the most common microdeletion syndrome and seen at a prevalence of 1 in 4000 to 6000 live births [1]. It is characterized by hemizygous microdeletion of ≤3 mb size of chromosome 22q11.2 locus in which several genes are lost. It is mostly spontaneous/de novo and in <10% cases are inherited [2–4]. It is frequently associated with multiple congenital anomalies, in partic- ular cardiac anomaly (conotruncal cardiac anomaly such as Fallot’s tetralogy, interrupted aortic arch, truncus arte- riosus, or major aortopulmonary collateral), developmental delay, hypocalcaemia, immune defciency, clef palate or velopharyngeal insufciency or swallowing difculty, and dysmorphism (broad bulbous nose, square shaped tip of nose, short philtrum, telecanthus, slanting eyes, low set ears, etc.). FISH, until recent, was commonly used for precise genetic diagnosis of common microdeletion syndromes, including 22q11.2 microdeletion [5–8]. However, FISH provides infor- mation only on targeted locations and does not allow a comprehensive evaluation of the whole genome. In addition, atypical smaller deletions are difcult to identify by FISH due to failure in covering those locations by single FISH probe (outside the region of hybridisation by the FISH probe). Fur- thermore, it is difcult to detect 22q11.2 duplication by FISH due to variable size of signals as well as distraction with split signals of normal cells. Ofen 22q11.2 duplication displays features like 22q11.2 deletion syndrome [9]. Hence, FISH alone cannot provide reliable diagnosis for cases of 22q11.2 microdeletions/duplications syndrome. Further, if FISH is used for doubtful cases (if few numbers of clinical criteria are fulflled by patient) then chances of detecting targeted deletion are less frequent [7, 8]. High-resolution array CGH was used to investigate FISH negative for 22q11.2 deletions cases with conotruncal heart defects [10] and additional cases of 22q11.2 microdeletion/microduplication containing TBX1 gene were detected. In this study with SNP microarray we have assessed 101 cases of FISH negative/noninformative clinically suspected 22q11.2 microdeletion syndrome to deter- mine whether any beneft is gained from using SNP microar- ray. Hindawi Publishing Corporation Scientifica Volume 2016, Article ID 5826431, 18 pages http://dx.doi.org/10.1155/2016/5826431