Analysis of the Prader-Willi syndrome imprinting center using droplet digital PCR and next-generation whole-exome sequencing

Molecular Genetics & Genomic Medicine
Samantha N HartinMerlin G Butler

Abstract

Detailed analysis of imprinting center (IC) defects in individuals with Prader-Willi syndrome (PWS) is not readily available beyond chromosomal microarray (MA) analysis, and such testing is important for a more accurate diagnosis and recurrence risks. This is the first feasibility study of newly developed droplet digital polymerase chain reaction (ddPCR) examining DNA copy number differences in the PWS IC region of those with IC defects. The study cohort included 17 individuals without 15q11-q13 deletions or maternal disomy but with IC defects as determined by genotype analysis showing biparental inheritance. Seven sets of parents and two healthy, unrelated controls were also analyzed. Copy number differences were distinguished by comparing the number of positive droplets detected by IC probes to those from a chromosome 15 reference probe, GABRβ3. The ddPCR findings were compared to results from other methods including MA, and whole-exome sequencing (WES) with 100% concordance. The study also estimated the frequency of IC microdeletions and identified gene variants by WES that may impact phenotypes including CPT2 and NTRK1 genes. Droplet digital polymerase chain reaction is a cost-effective method that can be used to confirm th...Continue Reading

References

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Oct 5, 2007·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Yuan-Wei ZhangGary Rudnick
Aug 14, 2008·American Journal of Medical Genetics. Part a·H L NewkirkM G Butler
Jun 19, 2009·The Journal of Investigative Dermatology·Jamison D FeramiscoHensin Tsao
Nov 2, 2011·Current Genomics·Merlin G Butler
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Jun 12, 2016·Progress in Molecular Biology and Translational Science·Merlin G Butler
Feb 14, 2018·American Journal of Medical Genetics. Part a·Samantha N HartinMerlin G Butler
Oct 6, 2018·American Journal of Medical Genetics. Part a·Merlin G ButlerPartha C Krishnamurthy

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Citations

Jun 2, 2020·Frontiers in Pediatrics·Merlin G Butler, Jessica Duis
Jul 8, 2020·International Journal of Molecular Sciences·Ann Genovese, Merlin G Butler
Jan 11, 2020·Frontiers in Endocrinology·Régis Afonso CostaLetícia da Cunha Guida
Feb 11, 2021·Sleep Medicine Reviews·Matteo CataldiLino Nobili
Jun 3, 2021·Reproductive Sciences·Xiao-Qun LiuGuo-Can Yang
May 29, 2021·Frontiers in Genetics·Samuel P StromMerlin G Butler

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Methods Mentioned

BETA
PCR

Software Mentioned

SAM tools
Genome Analysis Toolkit ( GATK )
BWA [ Aligner ]
QuantaSoft Analysis Pro
BWA
TapeStation
BaseSpace Workflow ]
PolyPhen
Burrows Aligner ( BWA )
Affymetrix

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