?一种数学进展提高了人类基因组测序的能力，这为肿瘤生物学提供了一种比传统DNA测序法快速和高性价比的新工具。
??USC的分子和计算生物学教授Michael Waterman小组的学生最近发展了一种数学运算来处理限制性内切酶图谱技术得到的大量数据。这种方法又被叫做“可见图谱”。
??可见图谱技术在染色体上得到坐标，这就像高速公路上的公里牌一样。Standford大学博士后，文章第一作者Anton Valouev表示，这种算法使得可见图谱技术可被用于人类基因组。他说：“这为医学应用提供了极大的便利，特别是寻找基因组异常方面。”
??这一结果发表在上周的《Proceeding of the National Academy of Science》上。
??可见图谱技术是上世纪90年代末由Wisconsin-Madison大学化学和基因学教授David Schwartz发明的，这种技术能检测基因组的大小和大尺度的结构。它利用荧光显微镜对用酶分离的单个DNA分子成像。对大量DNA成像后，就可以得到基因组图谱了。
??可见图谱技术缺少基因组序列的微小细节，但是这可以用其它手段补偿。基因学家常说99.9%的人类DNA是一致的，但有时我们会发现一些区域有很大的改变。这些改变包括大片基因结构的缺失或多余。癌症基因就具有这样的特征。
??作者之一的Philip Green说：“这很难被传统方法检测到。”而可见图谱技术可以得到基因组的长度，以及快速检测结构和长度上的差别。将以上结果和正常基因组比较就能知道变异是否发生。
英文原文：
Genome ID Method Extended to Humans
A mathematical discovery has extended the reach of a novel genome mapping method to humans, potentially giving cancer biology a faster and more cost-effective tool than traditional DNA sequencing.
student-led group from the laboratory of Michael Waterman, University Professor in molecular and computational biology in USC College, has developed an algorithm to handle the massive amounts of data created by a restriction mapping technology known as “optical mapping.”
Restriction maps provide coordinates on chromosomes analogous to mile markers on freeways.
Lead author Anton Valouev, a recent graduate of Waterman’s lab and now a postdoctoral fellow at Stanford University, said the algorithm makes it possible to optically map the human genome.
“It carries tremendous benefits for medical applications, specifically for finding genomic abnormalities,” he said.
The algorithm appears in this week’s PNAS Early Edition.
Optical mapping was developed at New York University in the late 1990s by David Schwartz, now a professor of chemistry and genetics at the University of Wisconsin-Madison. Schwartz and a collaborator at Wisconsin, Shiguo Zhou, co-authored the PNAS paper.
The power of optical mapping lies in its ability to reveal the size and large-scale structure of a genome. The method uses fluorescence microscopy to image individual DNA molecules that have been divided into orderly fragments by so-called restriction enzymes.
By imaging large numbers of an organism’s DNA molecules, optical mapping can produce a map of its genome at a relatively low cost.
An optical map lacks the minute detail of a genetic sequence, but it makes up for that shortcoming in other ways, said Philip Green, a professor of genome sciences at the University of Washington who edited the PNAS paper.
Geneticists often say that humans have 99.9 percent of their DNA in common. But, Green said, “individuals occasionally have big differences in their chromosome structure. You sometimes find regions where there are larger changes.”
Such changes could include wholesale deletions of chunks of the genome or additions of extra copies. Cancer genomes, in particular, mutate rapidly and contain frequent abnormalities.
“That’s something that’s very hard to detect” by conventional sequencing, Green said, adding that sequencing can simply miss part of a genome.
Optical mapping, by contrast, can estimate the absolute length of a genome and quickly detect differences in length and structure between two genomes. Comparing optical maps of healthy and diseased genomes can guide researchers to crucial mutations.
Though he called optical mapping “potentially very powerful,” Green added that it requires such a high level of expertise that only a couple of laboratories in the world use the method.
