scholarly journals Deep sequencing of GDF5 reveals the absence of rare variants at this important osteoarthritis susceptibility locus

2011 ◽  
Vol 19 (4) ◽  
pp. 430-434 ◽  
Author(s):  
A.W. Dodd ◽  
C. Rodriguez-Fontenla ◽  
M. Calaza ◽  
A. Carr ◽  
J.J. Gomez-Reino ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Rare Variants ◽  
Susceptibility Locus

scholarly journals Introduction to Deep Sequencing and Its Application to Drug Addiction Research with a Focus on Rare Variants

2013 ◽  
Vol 49 (1) ◽  
pp. 601-614 ◽  
Author(s):  
Shaolin Wang ◽  
Zhongli Yang ◽  
Jennie Z. Ma ◽  
Thomas J. Payne ◽  
Ming D. Li
Keyword(s):  
Drug Addiction ◽  
Deep Sequencing ◽  
Rare Variants

scholarly journals O3-13-03: THE ROLE OF ZCWPW1 SUSCEPTIBILITY LOCUS RARE VARIANTS IN ALZHEIMER'S DISEASE

2019 ◽  
Vol 15 ◽  
pp. P920-P920
Author(s):  
Fahri Küçükali ◽  
Katrin Nußbaumer ◽  
Jasper Van Dongen ◽  
Elisabeth Hens ◽  
Christine Van Broeckhoven ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Rare Variants ◽  
Susceptibility Locus

Identification Of New Rare Variants Associated With Familial Autoimmune Thyroid Diseases By Deep Sequencing Of Linked Loci

2021 ◽  
Author(s):  
Cheuk Wun Li ◽  
Ravi Sachidanandam ◽  
Anitha Jayaprakash ◽  
Zhengzi Yi ◽  
Weijia Zhang ◽  
...  
Keyword(s):  
Genetic Susceptibility ◽  
Deep Sequencing ◽  
Rare Variants ◽  
Thyroid Autoimmunity ◽  
Susceptibility Genes ◽  
Thyroid Diseases ◽  
Phosphoglycerate Mutase ◽  
Inositol Polyphosphate ◽  
Autoimmune Thyroid Diseases ◽  
Autoimmune Thyroid

Abstract Context Genetic risk factors play a major role in the pathoetiology of autoimmune thyroid diseases (AITD). So far, only common risk variants have been identified in AITD susceptibility genes. Recently, rare genetic variants have emerged as important contributors to complex diseases, and we hypothesized that rare variants play a key role in the genetic susceptibility to AITD. Objective To identify new rare variants that are associated with familial AITD. Design We performed deep sequencing of 3 previously mapped AITD-linked loci (10q, 12q, and 14q) in a dataset of 34 families in which AITD clustered (familial AITD). Results We identified 13 rare variants, located in the inositol polyphosphate multikinase (IPMK) gene, that were associated with AITD (i.e. both Graves’ disease [GD] and Hashimoto’s thyroiditis [HT]); two rare variants, within the dihydrolipoamide S-succinyltransferase (DLST) and zinc-finger FYVE domain-containing protein (ZFYVE1) genes, that were associated with GD only; and 3 rare variants, within the phosphoglycerate mutase 1 pseudogene 5 (PGAM1P5), LOC105369879, and methionine aminopeptidase 2 (MetAP2) genes, that were associated with HT only. Conclusion Our study demonstrates that, in addition to common variants, rare variants also contribute to the genetic susceptibility to AITD. We identified new rare variants in 6 AITD susceptibility genes that predispose to familial AITD. Of them three genes, IPMK, ZFYVE1, and MetAP2, are mechanistically involved in immune pathways and have been previously shown to be associated with autoimmunity. These genes predispose to thyroid autoimmunity and may in the future serve as potential therapeutic targets.

scholarly journals UGT1A1 Genetic Variations and a Haplotype Associated with Neonatal Hyperbilirubinemia in Indonesian Population

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Dewi A. Wisnumurti ◽  
Yunia Sribudiani ◽  
Robert M. Porsch ◽  
Ani M. Maskoen ◽  
Lola I. Abdulhamied ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Haplotype Analysis ◽  
Rare Variants ◽  
Neonatal Hyperbilirubinemia ◽  
Common Finding ◽  
Common Variants ◽  
Indonesian Population ◽  
Novel Variants ◽  
Targeted Deep Sequencing ◽  
Deep Sequencing Approach

Neonatal hyperbilirubinemia (NH) is a common finding in newborn babies in Indonesia. Common and rare variants of UGT1A1 have been known to contribute to NH etiology. This study aims to identify UGT1A1 genetic variation and haplotype associated with NH in Indonesian population. DNA was isolated from 116 cases and 115 controls and a targeted-deep sequencing approach was performed on the promoter, UTRs, and exonic regions of UGT1A1. Determining association of common variants and haplotype analysis were performed using PLINK and Haploview. Ten and 4 rare variants were identified in cases and controls, respectively. The UGT1A1 rare variants frequency in cases (5.17%) was higher than that in controls (1.7%). Four of those rare variants in cases (p.Ala61Thr, p.His300Arg, p.Lys407Asn, and p.Tyr514Asn) and three in controls (p.Tyr79X, p.Ala346Val, and p.Thr412Ser) are novel variants. The frequencies of p.Gly71Arg, p.Pro229Gln, and TA7 common variants were not significantly different between cases and controls. A haplotype, consisting of 3 major alleles of 3′ UTRs common variants (rs8330C>G, rs10929303C>T, and rs1042640C>G), was associated with NH incidence (p=0.025) in this population. Using targeted-deep sequencing and haplotype analysis, we identified novel UGT1A1 rare variants and disease-associated haplotype in NH in Indonesian population.

scholarly journals Error rates, PCR recombination, and sampling depth in HIV-1 Whole Genome Deep Sequencing

2016 ◽  
Author(s):  
Fabio Zanini ◽  
Johanna Brodin ◽  
Jan Albert ◽  
Richard A. Neher
Keyword(s):  
Deep Sequencing ◽  
Large Scale ◽  
Rare Variants ◽  
Cost Effective ◽  
Data Interpretation ◽  
Error Rates ◽  
Whole Genome ◽  
Viral Genomes ◽  
Sequencing Errors ◽  
Hiv 1

Deep sequencing is a powerful and cost-effective tool to characterize the genetic diversity and evolution of virus populations. While modern sequencing instruments readily cover viral genomes many thousand fold and very rare variants can in principle be detected, sequencing errors, amplification biases, and other artifacts can limit sensitivity and complicate data interpretation. Here, we describe several control experiments and error correction methods for whole-genome deep sequencing of viral genomes. We developed many of these in the course of a large scale whole genome deep sequencing study of HIV-1 populations. We measured the substitution and indel errors that arose during sequencing and PCR and quantified PCR-mediated recombination. We find that depending on the viral load in the samples, rare mutations down to 0.2% can be reproducibly detected. PCR recombination can be avoided by consistently working at low amplicon concentrations.

New susceptibility locus for NIDDM is localized to human chromosome 20q

Diabetes ◽  
1997 ◽  
Vol 46 (5) ◽  
pp. 876-881 ◽  
Author(s):  
L. Ji ◽  
M. Malecki ◽  
J. H. Warram ◽  
Y. Yang ◽  
S. S. Rich ◽  
...  
Keyword(s):  
Human Chromosome ◽  
Susceptibility Locus
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