Additional file 1: Table S1. of SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads

Spoligotype prediction and time performance of 161 Mtb isolates with SpoTyping in comparison with SpolPred. Table S2. Spoligotypes of 14 Mtb isolates determined from contigs obtained by de novo assembly, Velvet. Table S3. Actual length at different percentiles used as the read length for SpolPred spoligotype prediction of isolates sequenced on Illumina MiSeq. Table S4. Spoligotype prediction for Mtb isolates sequenced by Illumina MiSeq with SpoTyping in comparison with SpolPred. Table S5. Actual length at different percentiles used as the read length for SpolPred spoligotype prediction of isolates sequenced on Ion Torrent. Table S6. Spoligotype prediction for Mtb isolates sequenced by Ion Torrent with SpoTyping in comparison with SpolPred. Table S7. Statistics of time and accuracy of running SpoTyping on 50 iterations each for various down-sampling ratios of an H37Ra Mtb isolate. Table S8. Statistics of time and accuracy of running SpoTyping on 50 iterations each for various down-sampling ratios of a Beijing Mtb isolate. Table S9. Lineages of 14 discordant Mtb isolates by SpoTyping, experimentally reported and phylogenetic tree. (XLSX 55 kb

Can Evidence from Genome-Wide Association Studies and Positive Natural Selection Surveys Be Used to Evaluate the Thrifty Gene Hypothesis in East Asians?

<div><p>Body fat deposition and distribution differ between East Asians and Europeans, and for the same level of obesity, East Asians are at higher risks of Type 2 diabetes (T2D) and other metabolic disorders. This observation has prompted the reclassifications of body mass index thresholds for the definitions of “overweight” and “obese” in East Asians. However, the question remains over what evolutionary mechanisms have driven the differences in adiposity morphology between two population groups that shared a common ancestor less than 80,000 years ago. The Thrifty Gene hypothesis has been suggested as a possible explanation, where genetic factors that allowed for efficient food-energy conversion and storage are evolutionarily favoured by conferring increased chances of survival and fertility. Here, we leveraged on the existing findings from genome-wide association studies and large-scale surveys of positive natural selection to evaluate whether there is currently any evidence to support the Thrifty Gene hypothesis. We first assess whether the existing genetic associations with obesity and T2D are located in genomic regions that are reported to be under positive selection, and if so, whether the risk alleles sit on the extended haplotype forms. In addition, we interrogate whether these risk alleles are the derived forms that differ from the ancestral alleles, and whether there is significant evidence of population differentiation at these SNPs between East Asian and European populations. Our systematic survey did not yield conclusive evidence to support the Thrifty Gene hypothesis as a possible explanation for the differences observed between East Asians and Europeans.</p></div

F_ST scores between pairs of East Asian and European populations at three index SNPs around <i>THADA</i> and on chromosome 7 in the cluster of genes containing <i>GCC1</i>, <i>ARF5</i>, <i>PAX4</i> and <i>SND1</i>.

<p>Population abbreviations represent: CEU – Utah residents with Northern and Western European ancestry from the CEPH collection; CHB – Han Chinese in Beijing, China; CHD – Chinese in Metropolitan Denver, Colorado; JPT – Japanese in Toyko, Japan; MXL – Mexican ancestry in Los Angeles, California; TSI – Toscani in Italia.</p><p>F_ST scores between pairs of East Asian and European populations at three index SNPs around <i>THADA</i> and on chromosome 7 in the cluster of genes containing <i>GCC1</i>, <i>ARF5</i>, <i>PAX4</i> and <i>SND1</i>.</p

Positively selected Type 2 diabetes associated SNPs from genome-wide association studies (GWAS).

<p>Summary of six SNPs reported to be associated with Type 2 diabetes from the GWAS catalogue maintained by the National Human Genome Research Institute (NHGRI), accessed on 30^th June 2013, that are located in genomic regions that are putatively under positive selection in at least one of 14 populations from the International HapMap Project and the Singapore Genome Variation Project.</p>a<p>Ancestral allele.</p><p>Positively selected Type 2 diabetes associated SNPs from genome-wide association studies (GWAS).</p

Long haplotypes around two T2D-associated SNPs in East Asian and European populations.

<p>Illustration of haplotype forms identified by haploPS that span the longest genetic distance around two SNPs rs6467136 and rs10229583 that are located around a cluster of four genes on chromosome 7 (brown horizontal bars: <i>GCC1</i>, <i>ARF5</i>, <i>PAX4</i>, <i>SND1</i>). The figure shows the uncharacteristically long haplotypes that were present at a haplotype frequency of 40% in the four East Asian populations (CHB, CHD, CHS, JPT), together with the longest haplotypes present in the European populations (CEU, TSI, MXL) that were comparatively much shorter and did not yield significant evidence of positive selection. The haplotypes for the four East Asian populations carried both risk alleles at the two SNPs that have been reported in association studies to increase the risk to Type 2 diabetes.</p

Long haplotype regions (specific to East Asians) containing trait associated SNPs.

<p>Three SNPs from three genomic regions associated with T2D in or near <i>ARF5, PAX4, SND1, GCC1, C2CD4A,</i> and <i>C2CD4B</i> genes, which meet the criteria that both the evidence of T2D association and positive selection (haploPS score <0.05) were specific to only East Asians. The allele that increases the risk of T2D is identified and interrogated whether it (i) matches the ancestral allelic form on the chimpanzee genome, and/or (ii) sits on the positively selected haplotype form.</p>a<p>Ancestral allele.</p><p>Long haplotype regions (specific to East Asians) containing trait associated SNPs.</p

Long haplotypes around <i>THADA</i> in East Asian and European populations.

<p>Illustration of haplotype forms identified by haploPS that span the longest genetic distances around <i>THADA</i> (brown horizontal bar) on chromosome 2. Uncharacteristically long haplotypes were found at the same frequency of 45% in two East Asian populations (CHD, CHS) to span <i>THADA</i>, whereas at the same frequency, the longest haplotypes present in European populations (CEU, TSI, MXL) were comparatively much shorter. The haplotypes for the two East Asian populations also carried the thymine allele at rs7578597 that has been reported in association studies to increase the risk to Type 2 diabetes.</p

The LOESS fitting of the clockwise and counter-clockwise distributions that achieved equilibrium.

<p>The letters correspond to the simulations given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010464#pone-0010464-t002" target="_blank">table 2</a>.</p

The <i>E. coli</i> simulation system.

<p>The <i>E. coli</i> simulation system.</p

Statistical closeness between the simulations and the experimental data.

<p>Statistical closeness between the simulations and the experimental data.</p