Wednesday, April 16, 2003

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Bio-IT World The Complete Gene Set as the Key Data Connector

"The real surprise, of course, was this issue about the number of genes. At first, we weren't so sure about the new, lower estimate [~30,0000], but there is an increasing degree of confidence in it. People are still finding genes, and some people have reported finding very many. But there is more than one explanation for that. For example, there are clearly a lot of pseudogenes in the genome -- sequences derived from a functional gene but that are no longer functional.

Part of this uncertainty about the number of genes is because of the state of gene prediction."

redux [06.05.02]
UniSci Chromosome 21 Contains 10% More Genes Than Predicted

"Re-analyzing the same chromosome through a different technique, researchers at the University of Geneva and the Ludwig Institute for Cancer Research found that chromosome 21 contains roughly 10% more genes than were either confirmed or predicted.

"This demonstrates why we cannot rely on gene prediction alone to identify all human genes," said the study's lead author, Dr. Stylianos Antonarakis, of the Division of Medical Genetics at the University of Geneva Medical School. "Getting the right number of genes is crucial if we hope to use this information to fight disease.""

redux [10.11.01]
The Scientist Human Genes: How Many?
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"Counting human genes ought to be straightforward. Tracking telltale signs--motifs for promoters, translation start sites, splice sites, CpG islands--gene counters must by now be mopping up, finalizing chromosomal locations of every human gene already known, and predicting whereabouts of all the rest. Insert one human genome sequence, turn the bioinformatics crank, and genes gush out like a slot machine jackpot, right?

"No, no, no," says Bo Yuan, of Ohio State University, having a laugh over the idea that computation is all you need to tally genes. To the contrary, states the director of the bioinformatics group in the division of Human Cancer Genetics at Ohio State, trawling for genes is so labor-intensive that several years may pass before researchers possess a highly accurate count."

redux [08.24.01]
The New York Times Human Genome Now Appears More Complicated After All
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"After a humiliating deflation this February, human dignity is on the recovery path, at least as measured by the number of genes in the human genome.

Two new estimates put the likely number of human genes at around 40,000, up by a third from the estimate of about 30,000 in February by the two teams of scientists who decoded the human genome. The low estimate still has its defenders."

NPR: All Things Considered DNA Recount

"Recent estimates that the human genome consists of only about 30,000 genes may be way off the mark, according to a study published today in the journal Cell. NPR's Richard Harris has the story. (3:45)"

redux [01.18.01]
BBC Dispute over number of human genes

"Two rival teams that cracked the human genome may have underestimated the number of human genes, according to a new computer analysis."

Scientists in the United States claim humans are built from 66,000 genes, nearly twice as many as the current consensus."

"But the new analysis, published on the website of the journal Genome Biology, has been dismissed by the Sanger Centre, in Cambridgeshire, UK, which was responsible for about a third of the human genome sequencing effort."

""The experimental evidence actually points to 30-40,000 genes," Dr Hubbard told BBC News Online. "I don't believe the argument in this paper that there are a lot more genes. This is an entirely computational paper and I don't think it's very credible.""

redux [11.13.00]
BioMedNet UK geneticist offers exact count of human genes
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"If James Watson, co-discoverer of DNA's structure, says we don't know how many genes there are, you're inclined to believe him. So it was a great surprise to hear the legend denounced, albeit with due deference. At the last count, insisted Kay Davies, professor of anatomy at the University of Oxford, humans are reckoned to have 40,944 tiny protein factories.

She was drawing on statistics that define the proteome, the protein equivalent of the genome, as the set of all expressed proteins in humans, for which 40,944 genes are individually responsible. Not a huge figure, she noted, barely the equivalent of three flies or a couple of worms. "Apologies Jim, let's talk over tea," she added."

redux [05.13.00]
Wired News Amped Geneticists Bet on Genome

"Well, they weren't all men, but mostly. The betting in the pub continued, the lowest bet being 29,800 genes placed by Pat Tome and the highest number coming from John Quackenbush at 118,259.

The pool was organized by Erwin Birney, a team leader at the European Bioinformatics Institute. He tried to convince the bartender to oversee the betting, but was told in no uncertain terms that no gambling was allowed in the Cold Spring bar.

Guesses on the number of genes in the human genome have lowered considerably since the mapping of chromosome 21, which researchers found to contain only 225 genes, far fewer than previously predicted. The researchers on the chromosome 21 study predicted their results could mean that there are as few as 40,000 genes in the entire human genome.

"Someone from Incyte will probably show up and bet 150,000," one gambler said."