HTSeq-Hadoop: Extending HTSeq for Massively Parallel Sequencing Data Analysis Using Hadoop

2014 ◽  
Author(s):  
Alexey Siretskiy ◽  
Ola Spjuth
Keyword(s):  
Data Analysis ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Sequencing Data ◽  
Parallel Sequencing ◽  
Sequencing Data Analysis

scholarly journals Noninvasive Prenatal Diagnosis of Monogenic Diseases by Targeted Massively Parallel Sequencing of Maternal Plasma: Application to β-Thalassemia

2012 ◽  
Vol 58 (10) ◽  
pp. 1467-1475 ◽  
Author(s):  
Kwan-Wood G Lam ◽  
Peiyong Jiang ◽  
Gary J W Liao ◽  
K C Allen Chan ◽  
Tak Y Leung ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Massively Parallel Sequencing ◽  
Globin Gene ◽  
Maternal Plasma ◽  
Massively Parallel ◽  
Sequencing Data ◽  
Plasma Dna ◽  
Parallel Sequencing ◽  
Noninvasive Prenatal Diagnosis ◽  
Monogenic Diseases

Abstract BACKGROUND A genomewide genetic and mutational profile of a fetus was recently determined via deep sequencing of maternal plasma DNA. This technology could have important applications for noninvasive prenatal diagnosis (NIPD) of many monogenic diseases. Relative haplotype dosage (RHDO) analysis, a core step of this procedure, would allow one to elucidate the maternally inherited half of the fetal genome. For clinical applications, the cost and complexity of data analysis might be reduced via targeted application of this approach to selected genomic regions containing disease-causing genes. There is thus a need to explore the feasibility of performing RHDO analysis in a targeted manner. METHODS We performed target enrichment by using solution-phase hybridization followed by massively parallel sequencing of the β-globin gene region in 2 families undergoing prenatal diagnosis for β-thalassemia. We used digital PCR strategies to physically deduce parental haplotypes. Finally, we performed RHDO analysis with target-enriched sequencing data and parental haplotypes to reveal the β-thalassemic status for the fetuses. RESULTS A mean sequencing depth of 206-fold was achieved in the β-globin gene region by targeted sequencing of maternal plasma DNA. RHDO analysis was successful for the sequencing data obtained from the target-enriched samples, including a region in one of the families in which the parents had similar haplotype structures. Data analysis revealed that both fetuses were heterozygous carriers of β-thalassemia. CONCLUSIONS Targeted sequencing of maternal plasma DNA for NIPD of monogenic diseases is feasible.

scholarly journals SICTIN: Rapid footprinting of massively parallel sequencing data

2010 ◽  
Vol 3 (1) ◽  
Author(s):  
Stefan Enroth ◽  
Robin Andersson ◽  
Claes Wadelius ◽  
Jan Komorowski
Keyword(s):  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Sequencing Data ◽  
Parallel Sequencing

scholarly journals Detection of CYP2C19 Genetic Variants in Malaysian Orang Asli from Massively Parallel Sequencing Data

PLoS ONE ◽  
2016 ◽  
Vol 11 (10) ◽  
pp. e0164169 ◽  
Author(s):  
Geik Yong Ang ◽  
Choo Yee Yu ◽  
Vinothini Subramaniam ◽  
Mohd Ikhmal Hanif Abdul Khalid ◽  
Tuan Azlin Tuan Abdu Aziz ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Sequencing Data ◽  
Parallel Sequencing ◽  
Orang Asli

Estimating number of contributors in massively parallel sequencing data of STR loci

2019 ◽  
Vol 38 ◽  
pp. 15-22 ◽  
Author(s):  
Brian A Young ◽  
Katherine Butler Gettings ◽  
Bruce McCord ◽  
Peter M. Vallone
Keyword(s):  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Sequencing Data ◽  
Parallel Sequencing ◽  
Str Loci

A safe an easy method for building consensus HIV sequences from 454 massively parallel sequencing data

2018 ◽  
Vol 36 (2) ◽  
pp. 91-94
Author(s):  
Jose Ángel Fernández-Caballero Rico ◽  
Natalia Chueca Porcuna ◽  
Marta Álvarez Estévez ◽  
María del Mar Mosquera Gutiérrez ◽  
María Ángeles Marcos Maeso ◽  
...  
Keyword(s):  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Sequencing Data ◽  
Easy Method ◽  
Parallel Sequencing
Sign in / Sign up

Export Citation Format

Share Document