AIDec: An Algorithm for Detecting Allelic Imbalance Based on the Sequenom MassArray Platform

Author(s):  
Meng Wang
2014 ◽  
Author(s):  
Monika Migdalska-Sek ◽  
Karolina H Czarnecka ◽  
Michal Kusinski ◽  
Ewa Nawrot ◽  
Dorota Pastuszak-Lewandoska ◽  
...  

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Asia Mendelevich ◽  
Svetlana Vinogradova ◽  
Saumya Gupta ◽  
Andrey A. Mironov ◽  
Shamil R. Sunyaev ◽  
...  

AbstractA sensitive approach to quantitative analysis of transcriptional regulation in diploid organisms is analysis of allelic imbalance (AI) in RNA sequencing (RNA-seq) data. A near-universal practice in such studies is to prepare and sequence only one library per RNA sample. We present theoretical and experimental evidence that data from a single RNA-seq library is insufficient for reliable quantification of the contribution of technical noise to the observed AI signal; consequently, reliance on one-replicate experimental design can lead to unaccounted-for variation in error rates in allele-specific analysis. We develop a computational approach, Qllelic, that accurately accounts for technical noise by making use of replicate RNA-seq libraries. Testing on new and existing datasets shows that application of Qllelic greatly decreases false positive rate in allele-specific analysis while conserving appropriate signal, and thus greatly improves reproducibility of AI estimates. We explore sources of technical overdispersion in observed AI signal and conclude by discussing design of RNA-seq studies addressing two biologically important questions: quantification of transcriptome-wide AI in one sample, and differential analysis of allele-specific expression between samples.


2020 ◽  
Vol 102 ◽  
Author(s):  
Yael Laitman ◽  
Shay Tzur ◽  
Ruben Attali ◽  
Amit Tirosh ◽  
Eitan Friedman

Abstract Pheochromocytoma (PCC) is a rare, mostly benign tumour of the adrenal medulla. Hereditary PCC accounts for ~35% of cases and has been associated with germline mutations in several cancer susceptibility genes (e.g., KIF1B, SDHB, VHL, SDHD, RET). We performed whole-exome sequencing in a family with four PCC-affected patients in two consecutive generations and identified a potential novel candidate pathogenic variant in the REXO2 gene that affects splicing (c.531-1G>T (NM 015523.3)), which co-segregated with the phenotype in the family. REXO2 encodes for RNA exonuclease 2 protein and localizes to 11q23, a chromosomal region displaying allelic imbalance in PCC. REXO2 protein has been associated with DNA repair, replication and recombination processes and thus its inactivation may contribute to tumorigenesis. While the study suggests that this novel REXO2 gene variant underlies PCC in this family, additional functional studies are required in order to establish the putative role of the REXO2 gene in PCC predisposition.


PLoS ONE ◽  
2019 ◽  
Vol 14 (6) ◽  
pp. e0217765
Author(s):  
Jesper R. Gådin ◽  
Alfonso Buil ◽  
Carlo Colantuoni ◽  
Andrew E. Jaffe ◽  
Jacob Nielsen ◽  
...  

2011 ◽  
Vol 240 (5) ◽  
pp. 1163-1172 ◽  
Author(s):  
Ian C. Dunn ◽  
I. Robert Paton ◽  
Allyson K. Clelland ◽  
Sujith Sebastian ◽  
Edward J. Johnson ◽  
...  

Neoplasia ◽  
2002 ◽  
Vol 4 (5) ◽  
pp. 424-431 ◽  
Author(s):  
Phillippa J. Neville ◽  
David V. Contit ◽  
Pamela L. Paris ◽  
Howard Levint ◽  
William J. Catalona ◽  
...  

2003 ◽  
Vol 106 (1) ◽  
pp. 74-77 ◽  
Author(s):  
Kerstin Rhiem ◽  
Annette Klein ◽  
Miriam Münch ◽  
Rene Kreutzfeld ◽  
Juliane Ramser ◽  
...  

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