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 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.
Kan
Takatsugu
T
Gastroenterology Division, Department of Medicine, Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Rm 106 Baltimore MD 21287.
Paun
Bogdan C
BC
Mori
Yuriko
Y
Sato
Fumiaki
F
Jin
Zhe
Z
Hamilton
James P
JP
Ito
Tetsuo
T
Cheng
Yulan
Y
David
Stefan
S
Olaru
Alexandru V
AV
Yang
Jian
J
Agarwal
Rachana
R
Abraham
John M
JM
Meltzer
Stephen J
SJ