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Abstract

April - June 2022 | Vol. 15 | Issue 2 | 11-18
Low-Pass Genome Sequencing: A Good Option for Detecting Copy Number Variations
Somya Srivastava, Shubha R Phadke
Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
Address for Correspondence Email: shubharaophadke@gmail.com
 
Abstract
Low-pass genome sequencing (LPGS) is a technique to detect copy number variants and map their breakpoints by using the technology of next-generation sequencing (NGS). Cytogenetic microarray (CMA) has a high resolution but is restricted to only those areas of the genome for which it has probes, thereby missing many duplications and deletions. Next-generation sequencing can identify single nucleotide changes. LPGS utilizes the strengths of NGS to empower the field of cytogenetics by helping in identifying accurate breakpoints of genes disrupted by chromosomal aberrations. Since it uses the existing infrastructure of NGS, it is cheaper, has high throughput, requires low input DNA, and has a quick turnaround time consequently making it an ideal technique for prenatal samples where time and amount of sample are crucial. Various studies have found good concordance between the results of CMA and LPGS. The yield of testing does not increase, rather the ability to identify copy number variants in areas without probe, better delineation of breakpoint, technical ease and low cost per sample is where LPGS proves to be useful. LPGS, however, is afflicted by the bane of short read length which plagues next generation sequencing. In this article we discuss the various methods of LPGS and its advantages and disadvantages, and its applicability in the clinical setting.
 
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