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Genomics In The Journals: Apr 26, 2012

NEW YORK (GenomeWeb News) – In BMC Genetics, Polish researchers report on the ancient DNA analysis that they used to take a peek back at social organization patterns in a native population in Peru prior to Columbus' journey to the Americas. The analysis relied on DNA from bone and tooth samples from 41 individuals found at six traditional burial sites, known as chullpas, in the Arequipa area of Peru. By looking at markers from the mitochondrial genome, Y chromosome, and autosomes, researchers discerned family relationships between individuals at each site, using that information to surmise clues about the broader societal structure in the Andean population at the time.

"Our results show that this community of llama and alpaca herders was (genetically) an extended patriarchal society," corresponding author Mateusz Baca, a researcher with the University of Warsaw's Center for Precolumbian Studies, said in a statement. "The use of chullpas as family graves is consistent with the idea of … communities based around strong kinship relationships."

American and Australian researchers resequenced the genomes of two bulls that have served as dairy cattle sires as part of an effort to track down trait-related haplotypes under selection in dairy cattle — work that they describe in the Proceedings of the National Academy of Sciences.

The group sequenced the genome of a bull known as "Chief" to around 7.3 times coverage and the genome of his son "Mark" to about 13.5 times coverage. In the process, they identified more than a million SNP differences between the bulls, both widely used as dairy sires. To assess the accuracy of their haplotype reconstruction method, the team compared these SNPs with variant patterns in the BovineSNP50 database. From there, they brought in genotype data for 1,149 of Chief's offspring to unearth chromosomal regions that seem to have been under selection in the dairy cattle, along with candidate SNPs suspected of contributing to traits such as milk production and disease resistance.

A study in Neuron is highlighting genetic ties between autism and fragile X syndrome.

Researchers from Cold Spring Harbor lab and elsewhere did exome sequencing on members of 343 families affected by autism spectrum disorder. Each of these families were enrolled through the Simons Simplex Collection and included one child with ASD, at least one unaffected sibling, and two unaffected parents.

Although de novo missense and synonymous mutations were found at comparable levels in affected and unaffected individuals, the team reported, coding sequences from individuals with ASD contained an over-representation of de novo alterations expected to produce premature stop codons, frame shift changes, or splice site glitches. And when they looked at the genes affected by these changes — or by copy number alterations identified in past ASD analyses — investigators found a subset of genes that overlapped with genes whose translation appears to be influenced by the fragile X mental retardation gene product.

"Our finding has important implications for therapy and shows that autism is in large part a molecular disorder of neuroplasticity, the mechanisms by which our nervous system adapts to change," CSHL researcher Michael Wigler, corresponding author on the study, said in a statement.

The spread of agriculture from southern Europe to northern parts of the continent involved migrants who have left their genetic mark in the region, according to a Science study.

Researchers from Sweden and Denmark sequenced and assessed nearly 250 million bases of genomic DNA from the ancient remains of three hunter-gather individuals and one individual from a nearby agricultural community, generating enough sequence in the process to look at the individuals' mitochondrial genomes, too. The samples were found in Scandinavia and estimated to be roughly 5,000 years old. Genetic patterns identified in the hunter-gatherers resembled those found in existing northern European populations, though they did not fall squarely into any one group. On the other hand, the Stone Age farmer was more closely related to populations now living in the Mediterranean.

"The results suggest that agriculture spread across Europe in concert with a migration of people," Uppsala University evolutionary biologist Pontus Skoglund, the study's first author, said in a statement. "If farming had spread solely as a cultural process, we would not expect to see a farmer in the north with such genetic affinity to southern populations."

In another Science study, two University of California at Berkeley researchers describe the approach they used to assess rates of evolution in free-living bacteria from environmental biofilms. Using samples obtained from the same acid mine drainage site in California over the span of almost a decade, the pair used metagenomic sequencing and genome analyses to characterize genetic patterns in Leptospirillum bacteria, the main bugs in the biofilms, over time. From the SNP patterns and estimated nucleotide substitution rate, for example, they defined six Leptospirillum genotypes in the acid mine drainage site samples and teased apart the mutations and recombinations that led to their emergence in that environment.

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.

The Scan

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While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.