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...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2007-01-01
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| Series: | Bioinformatics and Biology Insights |
| Online Access: | http://la-press.com/article.php?article_id=359 |
| _version_ | 1811210211036233728 |
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| 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 |
| 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 |
| author_sort | Takatsugu Kan |
| collection | DOAJ |
| 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 nonsynonymous), 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. |
| first_indexed | 2024-04-12T04:50:44Z |
| format | Article |
| id | doaj.art-ed1f1a4a1d604b43879d643952ebf0c4 |
| institution | Directory Open Access Journal |
| issn | 1177-9322 |
| language | English |
| last_indexed | 2024-04-12T04:50:44Z |
| publishDate | 2007-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Bioinformatics and Biology Insights |
| spelling | doaj.art-ed1f1a4a1d604b43879d643952ebf0c42022-12-22T03:47:18ZengSAGE PublishingBioinformatics and Biology Insights1177-93222007-01-011116Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA SequencingTakatsugu KanBogdan C. PaunYuriko MoriFumiaki SatoZhe JinJames P. HamiltonTetsuo ItoYulan ChengStefan DavidAlexandru V. OlaruJian YangRachana AgarwalJohn M. AbrahamStephen J. MeltzerWe 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 nonsynonymous), 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.http://la-press.com/article.php?article_id=359 |
| 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 Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing Bioinformatics and Biology Insights |
| title | 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_short | 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 |
| url | http://la-press.com/article.php?article_id=359 |
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