Evidence of transcription at polyT short tandem repeats

Bessière, Chloé; Saraswat, Manu; Grapotte, Mathys; Menichelli, Christophe; Ramilowski, Jordan A.; Severin, Jessica; Hayashizaki, Yoshihide; Itoh, Masayoshi; Hasegawa, Akira; Suzuki, Harukazu; Carninci, Piero; Hoon, Michiel de; Wasserman, Wyeth W.; Bréhélin, Laurent; Lecellier, Charles-Henri

doi:10.1101/634261

Cited by 3 publications

(3 citation statements)

References 78 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…11 TOMM40-5239 has additionally been identified as a transcriptional start site by the FANTOM project. 40 It is also possible, and perhaps likely, that the Our study further used WGS to genotype the TOMM40-5239 allele. Genotyping long microsatellite regions such as TOMM40-5239 can be challenging.…”

Section: Discussionmentioning

confidence: 99%

Use of local genetic ancestry to assess TOMM40 -523′ and risk for Alzheimer disease

Bussies

Rajabli

Griswold³

et al. 2020

Neurol Genet

View full text Add to dashboard Cite

ObjectiveHere, we re-examine TOMM40-5239 as a race/ethnicity-specific risk modifier for late-onset Alzheimer disease (LOAD) with adjustment for local genomic ancestry (LGA) in Apolipoprotein E (APOE) «4 haplotypes. MethodsThe TOMM40-5239 size was determined by fragment analysis and whole genome sequencing in homozygous APOE «3 and APOE «4 haplotypes of African (AF) or European (EUR) ancestry. The risk for LOAD was assessed within groups by allele size. ResultsThe TOMM40-5239 length did not modify risk for LOAD in APOE «4 haplotypes with EUR or AF LGA. Increasing length of TOMM40-5239 was associated with a significantly reduced risk for LOAD in EUR APOE e3 haplotypes. ConclusionsAdjustment for LGA confirms that TOMM40-5239 cannot explain the strong differential risk for LOAD between APOE e4 with EUR and AF LGA. Our study does confirm previous reports that increasing allele length of the TOMM40-5239 repeat is associated with decreased risk for LOAD in carriers of homozygous APOE e3 alleles and demonstrates that this effect is occurring in those individuals with the EUR LGA APOE e3 allele haplotype. : FA = fragment analysis; WGS = whole genome sequencing. Comparison of TOMM40-5239 genotyping results between WGS and FA. Allele sizes are listed as number of T's. and risk for Alzheimer disease ′ -523 TOMM40 Use of local genetic ancestry to assess This information is current as of March 3, 2020 Services Updated Information & http://ng.neurology.org/content/6/2/e404.full.html including high resolution figures, can be found at: References http://ng.neurology.org/content/6/2/e404.full.html##ref-list-1 This article cites 38 articles, 2 of which you can access for free at: Citations http://ng.neurology.org/content/6/2/e404.full.html##otherarticles This article has been cited by 1 HighWire-hosted articles: Subspecialty Collections http://ng.neurology.org//cgi/collection/association_studies_in_genetics Association studies in genetics http://ng.neurology.org//cgi/collection/alzheimers_disease Alzheimer's disease following collection(s): This article, along with others on similar topics, appears in the Permissions & Licensing http://ng.neurology.org/misc/about.xhtml#permissions its entirety can be found online at: Information about reproducing this article in parts (figures,tables) or in Reprints http://ng.neurology.org/misc/addir.xhtml#reprintsus Information about ordering reprints can be found online: reserved. Online

show abstract

Section: Discussionmentioning

confidence: 99%

Use of local genetic ancestry to assess TOMM40 -523′ and risk for Alzheimer disease

Bussies

Rajabli

Griswold³

et al. 2020

Neurol Genet

View full text Add to dashboard Cite

show abstract

“…REs contained in intronic and exonic regions will likely show tissue-specific patterns of expression similar to those of the genes in which they are contained. Intergenic REs may not be expressed at all, although recent work shows that transcription initiation at microsatellites is much more widespread than previously thought 75 . Choice of RNA-seq library preparation method also appears to impact the viability of STR analysis.…”

Section: Discussionmentioning

confidence: 91%

Detection of repeat expansions in large next generation DNA and RNA sequencing data without alignment

Fearnley

Bennett

Bahlo

2022

Sci Rep

View full text Add to dashboard Cite

Bioinformatic methods for detecting short tandem repeat expansions in short-read sequencing have identified new repeat expansions in humans, but require alignment information to identify repetitive motif enrichment at genomic locations. We present superSTR, an ultrafast method that does not require alignment. superSTR is used to process whole-genome and whole-exome sequencing data, and perform the first STR analysis of the UK Biobank, efficiently screening and identifying known and potential disease-associated STRs in the exomes of 49,953 biobank participants. We demonstrate the first bioinformatic screening of RNA sequencing data to detect repeat expansions in humans and mouse models of ataxia and dystrophy.

show abstract

“…REs contained in intronic and exonic regions will likely show tissue-specific patterns of expression similar to those of the genes in which they are contained. Intergenic REs may not be expressed at all, although recent work shows that transcription initiation at microsatellites is much more widespread than previously thought 73 . Choice of RNA-seq library preparation method also appears to impact the viability of STR analysis.…”

Section: Discussionmentioning

confidence: 91%

Ultrafast, alignment-free detection of repeat expansions in next-generation DNA and RNA sequencing data

Fearnley

Bennett

Bahlo

2021

Preprint

View full text Add to dashboard Cite

Short tandem repeat expansions are an established cause of diseases such as Huntington's disease. Bioinformatic methods for detecting repeat expansions in short-read sequencing have revealed new repeat expansions in humans. Current bioinformatic methods to detect repeat expansions require alignment information to identify repetitive motif enrichment at genomic locations. We present superSTR, an ultrafast method that does not require alignment, capable of efficiently processing DNA and RNA sequencing data. superSTR is applied to UK Biobank data to efficiently analyse 49,953 whole exomes in a screening experiment, identifying known mutations as well as diseases not previously associated with REs. superSTR also identifies repeat expansion motifs in RNAseq data, demonstrated in several disorders and cell lines. superSTR is a new tool for the most efficient repeat expansion detection currently possible and complements existing locus-specific, reference dependent repeat expansion analysis tools. superSTR is available from https://github.com/bahlolab/superSTR.

show abstract

Evidence of transcription at polyT short tandem repeats

Cited by 3 publications

References 78 publications

Use of local genetic ancestry to assess TOMM40 -523′ and risk for Alzheimer disease

Use of local genetic ancestry to assess TOMM40 -523′ and risk for Alzheimer disease

Detection of repeat expansions in large next generation DNA and RNA sequencing data without alignment

Ultrafast, alignment-free detection of repeat expansions in next-generation DNA and RNA sequencing data

Contact Info

Product

Resources

About