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Studies on human genome variation provide insight into disease


The International HapMap Project was initiated with the primary goal of facilitating medical studies and understanding the genomic basis for human diseases. To coordinate with the journal Nature’s publication describing the HapMap, the journal Genome Research is announcing a special issue entitled "Human Genome Variation," which is entirely devoted to studies using these data to provide insight into human biology and disease.

Predicting pregnancy success

Successful human reproduction and the maintenance of early pregnancy are dependent on a cluster of genes on chromosome 19 called the Luteinizing Hormone/Chorionic Gonadotropin Beta (LHB/CGB). During primate evolution, this cluster actively underwent numerous gene duplications and structural rearrangements, allowing the associated genes to acquire new biological functions.

In this month’s issue of Genome Research, Dr. Maris Laan and her colleagues report their analysis of the LHB/CGB cluster in three human populations: European Estonians, African Mandenka, and Chinese Han. They demonstrate how gene conversion was critical for shaping the genetic diversity of this region in humans.

"This study paves the way for examining an individual’s potential reproductive success based on sequence variants of the LHB/CGB genes," explains Laan. "We may be able to determine whether an individual is particularly susceptible to spontaneous abortions or reduced gonadal function, for example."

Maris Laan, Ph.D.
Research Professor, University of Tartu, Estonia
Phone: +372-53495258

X-ing out hereditary prostate cancer

According to the Prostate Cancer Foundation, one of every six American men develops prostate cancer, making it the most common form of non-skin cancer. Growing evidence suggests that there is a significant hereditary component to the disease, and one of the most strongly associated genomic regions lies on the X chromosome.

This X chromosomal region spans a cluster of five SPANX genes that are predominantly expressed in the testis and in certain tumors. In this month’s issue of Genome Research, Dr. Vladimir Larionov and his colleagues examined the genetic architecture of the SPANX cluster and showed how the region exhibited dynamic deletions, duplications, and gene conversion events, some of which may have resulted in the development of mutations involved in prostate cancer susceptibility.

"Because of the strong similarity among genes in this region, we had to develop a new technique for our mutational analysis, which we call TAR cloning," explains Larionov. "Using this method, we isolated the SPANX region from 200 individuals by recombination in yeast."

Based on their results, the authors speculate that predisposition to prostate cancer – at least in some individuals – is determined by the specific architecture of the SPANX gene cluster on the X chromosome. "We’re hoping to clarify which specific types of genomic rearrangements lead to prostate cancer susceptibility," says Larinov, "so that we can someday identify therapeutic targets for this disease."

Vladimir Larionov, Ph.D.
Head, Genome Structure and Function Section, National Cancer Institute
Phone: 301-496-7941

Genetic traffic in DiGeorge syndrome

One of the most common human genomic disorders, DiGeorge syndrome, occurs in one of every 2,000-4,000 live births and involves a deletion on chromosome 22. The deletion is mediated by rare repetitive sequences that flank genes crucial for proper development of the heart, face, and upper thorax.

Dr. Bernice Morrow and her colleagues describe in this month’s issue of Genome Research how they examined these flanking repetitive sequences for patterns of polymorphisms. "Our results show that there are intervals with more frequent traffic of genetic material – regions with higher rates of gene conversion or recombination – that are indicative of genomic instability," explains Morrow.

"With this knowledge in hand, we hope to screen our patients and identify the genomic mechanism underlying this important disease," says Morrow.

Bernice Morrow, Ph.D.
Professor, Albert Einstein College of Medicine
Phone: 718-430-4274

Looking for genes in all the right places

Geneticists rely on variation, or alterations in DNA sequence, for disease-association studies. Hereditary traits such as heart disease, arthritis, and Alzheimer’s can be assigned to specific genomic regions based on their association with DNA markers.

The success of disease-association studies is dependent upon several characteristics of the DNA markers, including allelic frequency and genomic coverage. In some cases, a particular variant at one locus is perfectly associated with a specific variant at another locus; in other words, the two markers are "genetically indistinguishable."

Dr. Lon Cardon and his colleagues describe in this month’s issue of Genome Research how these "genetically indistinguishable" polymorphisms can complicate the identification of disease-related genes. "Although they should pose few difficulties when they are located close together on the same chromosome, they often occur on different chromosomes, where it is quite another story," explains Cardon. When this is the case, true disease genes cannot be distinguished from their anonymous genetic ’twins.’

"Research in human genetic variation is rapidly moving towards realizing our aims of improving diagnosis of common diseases such as diabetes and heart disease," says Cardon, "but the genome is tricky; it won’t reveal its secrets easily. The real disease-causing culprits can have many silent partners. We need to know the relationships of all these partners to focus on real disease mutations and to minimize attention on the innocent gene variants that colour the humanity of life."

Lon R. Cardon, Ph.D.
Professor of Bioinformatics, University of Oxford
Phone: +44-01865-287591

Maria A. Smit | EurekAlert!
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