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This Week in Genome Research: Apr 1, 2015

A Spanish-led team takes a look at genome-wide DNA methylation patterns in multiple myeloma and in samples representing a pre-malignant condition that sometimes precedes it, known as monoclonal gammopathy of undetermined significance (MGUS). Using array-based methylome profiling, the researchers tested bone marrow plasma cells from 104 individuals with multiple myeloma and 16 individuals with MGUS. Through comparisons with methylation patterns in pooled normal samples from other bone marrow or tonsil sites, they found higher-than-usual methylation at enhancer sites that are also active during B-cell differentiation — findings they verified and expanded upon using reporter assays and sequencing methods.

The male sex chromosome seems to have experienced a strong bottleneck in diversity that was far more recent than the out-of-Africa migration. Researchers from Estonia, the UK, and elsewhere used Y chromosome sequence data for 456 individuals from around the world to reconstruct historical patterns for the Y chromosome. Their estimates put the most recent common Y chromosome ancestor at around 254,000 years old, followed by non-African haplogroup formation some 47,000 years to 52,000 years ago. But the data also suggests that there has been a Y chromosome bottleneck within the past 10,000 years, perhaps due to cultural pressures.

Finally, Pennsylvania State University researchers describe a computational method for typing short tandem repeats from short read sequencing data. The approach — known as the "short tandem repeat profiling using flank-based mapping," or STR-FM, pipeline — is intended to pick up all possible alleles for a given STR using tools integrated within Galaxy. For its proof-of-principle application of the STR-FM approach, the team used the strategy to assess error rates in both publicly available human genome sequence data and sequences produced in house. For instance, the study's authors saw far fewer errors for STRs sequenced using PCR-free protocols. They also started identifying long trinucleotide STRs that appear to coincide with particular diseases.