Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing

We performed high-throughput cDNA sequencing in colorectal adenocarcinoma and matching normal colorectal epithelium. All six hundred three genes in the UCSC database that were expressed in colon cancers and contained open reading frames of 1000 nucleotides or less were selected for study (total base...

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Main Authors:	Takatsugu Kan, Bogdan C. Paun, Yuriko Mori, Fumiaki Sato, Zhe Jin, James P. Hamilton, Tetsuo Ito, Yulan Cheng, Stefan David, Alexandru V. Olaru, Jian Yang, Rachana Agarwal, John M. Abraham, Stephen J. Meltzer M.D.
Format:	Article
Language:	English
Published:	SAGE Publishing 2007-01-01
Series:	Bioinformatics and Biology Insights
Online Access:	https://doi.org/10.1177/117793220700100001

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spelling	doaj-bbaf160474d842deaa0123f9d54de3b42020-11-25T03:15:43ZengSAGE PublishingBioinformatics and Biology Insights1177-93222007-01-01110.1177/117793220700100001Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA SequencingTakatsugu Kan0Bogdan C. Paun1Yuriko Mori2Fumiaki Sato3Zhe Jin4James P. Hamilton5Tetsuo Ito6Yulan Cheng7Stefan David8Alexandru V. Olaru9Jian Yang10Rachana Agarwal11John M. Abraham12Stephen J. Meltzer M.D.13Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.We performed high-throughput cDNA sequencing in colorectal adenocarcinoma and matching normal colorectal epithelium. All six hundred three genes in the UCSC database that were expressed in colon cancers and contained open reading frames of 1000 nucleotides or less were selected for study (total basepairs/bp, 366,686). 304,350 of these 366,686 bp (83.0%) were amplified and sequenced successfully. Seventy-eight sequence variants present in germline (i.e. normal) as well as matching somatic (i.e. tumor) DNA were discovered, yielding a frequency of 1 variant per 3,902 bp. Fifty-one of these sequence variants were homozygous (26 synonymous, 25 non-synonymous), while 27 were heterozygous (11 synonymous, 16 non-synonymous). Cancer tissue contained only one sequence-altered allele of the gene ATP50, which was present heterozygously alongside the wild-type allele in matching normal epithelium. Despite this relatively large number of bp and genes sequenced, no somatic mutations unique to tumor were found. High-throughput cDNA sequencing is a practical approach for detecting novel sequence variations and alterations in human tumors, such as those of the colon.https://doi.org/10.1177/117793220700100001
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Takatsugu Kan Bogdan C. Paun Yuriko Mori Fumiaki Sato Zhe Jin James P. Hamilton Tetsuo Ito Yulan Cheng Stefan David Alexandru V. Olaru Jian Yang Rachana Agarwal John M. Abraham Stephen J. Meltzer M.D.
spellingShingle	Takatsugu Kan Bogdan C. Paun Yuriko Mori Fumiaki Sato Zhe Jin James P. Hamilton Tetsuo Ito Yulan Cheng Stefan David Alexandru V. Olaru Jian Yang Rachana Agarwal John M. Abraham Stephen J. Meltzer M.D. Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing Bioinformatics and Biology Insights
author_facet	Takatsugu Kan Bogdan C. Paun Yuriko Mori Fumiaki Sato Zhe Jin James P. Hamilton Tetsuo Ito Yulan Cheng Stefan David Alexandru V. Olaru Jian Yang Rachana Agarwal John M. Abraham Stephen J. Meltzer M.D.
author_sort	Takatsugu Kan
title	Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing
title_short	Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing
title_full	Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing
title_fullStr	Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing
title_full_unstemmed	Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing
title_sort	rarity of somatic mutation and frequency of normal sequence variation detected in sporadic colon adenocarcinoma using high-throughput cdna sequencing
publisher	SAGE Publishing
series	Bioinformatics and Biology Insights
issn	1177-9322
publishDate	2007-01-01
description	We performed high-throughput cDNA sequencing in colorectal adenocarcinoma and matching normal colorectal epithelium. All six hundred three genes in the UCSC database that were expressed in colon cancers and contained open reading frames of 1000 nucleotides or less were selected for study (total basepairs/bp, 366,686). 304,350 of these 366,686 bp (83.0%) were amplified and sequenced successfully. Seventy-eight sequence variants present in germline (i.e. normal) as well as matching somatic (i.e. tumor) DNA were discovered, yielding a frequency of 1 variant per 3,902 bp. Fifty-one of these sequence variants were homozygous (26 synonymous, 25 non-synonymous), while 27 were heterozygous (11 synonymous, 16 non-synonymous). Cancer tissue contained only one sequence-altered allele of the gene ATP50, which was present heterozygously alongside the wild-type allele in matching normal epithelium. Despite this relatively large number of bp and genes sequenced, no somatic mutations unique to tumor were found. High-throughput cDNA sequencing is a practical approach for detecting novel sequence variations and alterations in human tumors, such as those of the colon.
url	https://doi.org/10.1177/117793220700100001
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Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing

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