Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnos...

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Autores principales:	Jason D Thompson, Gosuke Shibahara, Sweta Rajan, Joel Pel, Andre Marziali
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f1644f0d42be455bbf075a7f7d725893
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spelling	oai:doaj.org-article:f1644f0d42be455bbf075a7f7d7258932021-11-18T07:28:10ZWinnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.1932-620310.1371/journal.pone.0031597https://doaj.org/article/f1644f0d42be455bbf075a7f7d7258932012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22355378/?tool=EBIhttps://doaj.org/toc/1932-6203Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.Jason D ThompsonGosuke ShibaharaSweta RajanJoel PelAndre MarzialiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 2, p e31597 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jason D Thompson Gosuke Shibahara Sweta Rajan Joel Pel Andre Marziali Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.
description	Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.
format	article
author	Jason D Thompson Gosuke Shibahara Sweta Rajan Joel Pel Andre Marziali
author_facet	Jason D Thompson Gosuke Shibahara Sweta Rajan Joel Pel Andre Marziali
author_sort	Jason D Thompson
title	Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.
title_short	Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.
title_full	Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.
title_fullStr	Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.
title_full_unstemmed	Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.
title_sort	winnowing dna for rare sequences: highly specific sequence and methylation based enrichment.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/f1644f0d42be455bbf075a7f7d725893
work_keys_str_mv	AT jasondthompson winnowingdnaforraresequenceshighlyspecificsequenceandmethylationbasedenrichment AT gosukeshibahara winnowingdnaforraresequenceshighlyspecificsequenceandmethylationbasedenrichment AT swetarajan winnowingdnaforraresequenceshighlyspecificsequenceandmethylationbasedenrichment AT joelpel winnowingdnaforraresequenceshighlyspecificsequenceandmethylationbasedenrichment AT andremarziali winnowingdnaforraresequenceshighlyspecificsequenceandmethylationbasedenrichment
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Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

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