Sequence determinants of human microsatellite variability

Abstract

BackgroundMicrosatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their level of variability we have analyzed genotypes at 627 microsatellite loci in 1,048 worldwide individuals from the HGDP-CEPH cell line panel together with the DNA sequences of these microsatellites in the human RefSeq database.ResultsCalibrating PCR fragment lengths in individual genotypes by using the RefSeq sequence enabled us to infer repeat number in the HGDP-CEPH dataset and to calculate the mean number of repeats (as opposed to the mean PCR fragment length), under the assumption that differences in PCR fragment length reflect differences in the numbers of repeats in the embedded repeat sequences. We find the mean and maximum numbers of repeats across individuals to be positively correlated with heterozygosity. The size and composition of the repeat unit of a microsatellite are also important factors in predicting heterozygosity, with tetra-nucleotide repeat units high in G/C content leading to higher heterozygosity. Finally, we find that microsatellites containing more separate sets of repeated motifs generally have higher heterozygosity.ConclusionsThese results suggest that sequence properties of microsatellites have a significant impact in determining the features of human microsatellite variability.

lobSTR: A Short Tandem Repeat Profiler for Personal Genomes

“…Similar to STR studies with capillary platforms (Weber and Broman 2001), most of the errors were generated in dinucleotide STR loci, whereas other types of STRs showed moderate and similar error rates. The dinucleotide error rates presumably stem from two factors: First, these loci usually show the highest heterozygosity rates (Chakraborty et al 1997;Brinkmann et al 1998;Pemberton et al 2009). Therefore, they require on average more sequence reads to be correctly called.…”

“…Five genomes had a coverage of 1.43-1.93 with 109-bp reads, and the other seven had a coverage of 4.83-7.73 with 77-bp reads (Supplemental Table 3). One hundred and ninety-five STRs with equivalent entries in the lobSTR reference have been genotyped in these genomes using DNA electrophoresis as part of the CEPH-HGDP panel (Ramachandran et al 2005;Pemberton et al 2009). Combining lobSTR results from all data sets gave 59 comparable markers with a coverage of three to five reads with a median coverage of 33 (Supplemental Table 4).…”

“…stanford.edu/group/rosenberglab/repeatsDownload.html). The allelotypes were given as the number of repeats converted from PCR product size as described in Pemberton et al (2009). The repeat number is given as the reference repeat number plus the difference in product size from the reference divided by the motif size.…”

“…Using the STS marker table available from the UCSC Genome Browser, we converted the Pemberton et al (2009) markers to hg18 genomic coordinates and annotated them using the TRF table. lobSTR calls that are supported by three or more reads were converted to the Pemberton results.…”

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

“…Past technical constraints, however, limited the number of TRs that could be easily genotyped. For this reason, most TRbased studies of human diversity and intraspecies genetic divergence were restricted (Rosenberg et al 2002;Molla et al 2009;Pemberton et al 2009Pemberton et al , 2013Tishkoff et al 2009;Sun et al 2012) or focused on comparing reference genomes (Webster et al 2002;Kelkar et al 2008Kelkar et al , 2011Payseur et al 2011;Loire et al 2013). However, recent advances in sequencing methodology (for review, see Mardis 2008;Metzker 2010) and the development of novel software that can systematically genotype repeats at a genome-wide scale (for review, see Lim et al 2012) have permitted analysis of several thousand loci from multiple individuals in a cost-effective manner (McIver et al 2011(McIver et al , 2013Willems et al 2014).…”