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Detailed analysis o...
Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing
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- Höijer, Ida (author)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Medicinsk genetik och genomik
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- Tsai, Yu-Chih (author)
- Pacific Biosci, Menlo Pk, CA USA
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- Clark, Tyson A. (author)
- Pacific Biosci, Menlo Pk, CA USA
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- Kotturi, Paul (author)
- Pacific Biosci, Menlo Pk, CA USA
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- Dahl, Niklas (author)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Medicinsk genetik och genomik
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- Stattin, Evalena (author)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Medicinsk genetik och genomik,Uppsala Univ, Sci Life Lab, Dept Immunol Genet & Pathol, Uppsala, Sweden
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- Bondeson, Marie-Louise, 1960- (author)
- Uppsala universitet,Medicinsk genetik och genomik,Science for Life Laboratory, SciLifeLab
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- Feuk, Lars (author)
- Uppsala universitet,Medicinsk genetik och genomik,Science for Life Laboratory, SciLifeLab
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- Gyllensten, Ulf B. (author)
- Uppsala universitet,Medicinsk genetik och genomik,Science for Life Laboratory, SciLifeLab
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- Ameur, Adam (author)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för immunologi, genetik och patologi,Monash Univ, Sch Publ Hlth & Prevent Med, Melbourne, Vic, Australia
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(creator_code:org_t)
- 2018-07-12
- 2018
- English.
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In: Human Mutation. - : Hindawi Limited. - 1059-7794 .- 1098-1004. ; 39:9, s. 1262-1272
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Abstract
Subject headings
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- Amplification of DNA is required as a mandatory step during library preparation in most targeted sequencing protocols. This can be a critical limitation when targeting regions that are highly repetitive or with extreme guanine-cytosine (GC) content, including repeat expansions associated with human disease. Here, we used an amplification-free protocol for targeted enrichment utilizing the CRISPR/Cas9 system (No-Amp Targeted sequencing) in combination with single molecule, real-time (SMRT) sequencing for studying repeat elements in the huntingtin (HTT) gene, where an expanded CAG repeat is causative for Huntington disease. We also developed a robust data analysis pipeline for repeat element analysis that is independent of alignment of reads to a reference genome. The method was applied to 11 diagnostic blood samples, and for all 22 alleles the resulting CAG repeat count agreed with previous results based on fragment analysis. The amplification-free protocol also allowed for studying somatic variability of repeat elements in our samples, without the interference of PCR stutter. In summary, with No-Amp Targeted sequencing in combination with our analysis pipeline, we could accurately study repeat elements that are difficult to investigate using PCR-based methods.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Keyword
- amplification-free sequencing
- HTT
- Huntington disease
- No-Amp Targeted sequencing
- repeat expansion
- SMRT sequencing
- somatic mosaicism
- targeted enrichment
- targeted sequencing
Publication and Content Type
- ref (subject category)
- art (subject category)
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To the university's database
- By the author/editor
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Höijer, Ida
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Tsai, Yu-Chih
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Clark, Tyson A.
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Kotturi, Paul
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Dahl, Niklas
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Stattin, Evalena
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Bondeson, Marie- ...
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Feuk, Lars
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Gyllensten, Ulf ...
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Ameur, Adam
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- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Medical Genetics
- Articles in the publication
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Human Mutation
- By the university
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Uppsala University