Recent advances in sequencing technology make it possible to comprehensively catalogue genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. The amounts of raw data produced are prodigious and many computational steps are required to translate this output into high-quality variant calls. We present a unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs. Our process includes (1) initial read mapping; (2) local realignment around indels; (3) base quality score recalibration; (4) SNP discovery and genotyping to find all potential variants; and (5) machine learning to separate true segregating variation from machine artifacts common to next-generation sequencing technologies. We discuss the application of these tools, instantiated in the Genome Analysis Toolkit (GATK), to deep whole-genome, whole-exome capture, and multi-sample low-pass (~4×) 1000 Genomes Project datasets.

/pdf/a-framework-for-variation-discovery-and-genotyping-using-1mhes6klgp.pdf

A framework for variation discovery and genotyping using next-generation DNA sequencing data

We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.

/pdf/an-aboriginal-australian-genome-reveals-separate-human-4okveawg8r.pdf

An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia

Genome-wide association (GWA) studies have identified a large number of SNPs associated with disease phenotypes. As most GWA studies have been performed in populations of European descent, this Review examines the issues involved in extending the consideration of GWA studies to diverse worldwide populations. Although challenges exist with issues such as imputation, admixture and replication, investigation of a greater diversity of populations could make substantial contributions to the goal of mapping the genetic determinants of complex diseases for the human population as a whole.

/pdf/genome-wide-association-studies-in-diverse-populations-22qeq0c76r.pdf

Genome-wide association studies in diverse populations

Worldwide globalization and Westernization in social and economic aspects have led to drastic changes in South Korea during the past several decades. These changes include individual health behaviours, which were reflected as increased prevalence of non-communicable chronic diseases (NCDs), such as type 2 diabetes mellitus (T2DM), hypertension, obesity and cardiovascular disease (CVD). These NCDs are known to be caused by both environmental risk factors and predisposing genetic factors. Population decline is another issue in South Korea; the recorded fertility rate was 1.3 births per woman, and 10% of the population were elderly individuals aged 65 years according to the Population and Housing Census results of 2005-2010. We have also been observing an increased influx and efflux of the population due to globalization. In particular, there has been a rising tendency in the marriage-based inflow of South Asian women during the last decade. To attempt to solve public health issues resulting from these population trends and prepare for personalized and preventive health care in the future, the Korean government (National Research Institute of Health (NIH), Centers for Disease Control and Prevention and the Ministry of Health and Welfare, Korea) initiated a large prospective cohort study with government funding, named the Korean genome and epidemiology study (KoGES). The study is a consortium project consisting of six prospective cohort studies that would be categorized into population-based and geneenvironment model studies (Figure 1). The aim of the KoGES was to establish a genome epidemiological study platform for the research community with a health database and biobank, to investigate the genetic and environmental aetiology of common complex diseases in Koreans (i.e. T2DM, hypertension, obesity, metabolic syndrome, osteoporosis, CVD,and cancer) and causes of death with longterm follow-up. The ultimate goal of the KoGES was to develop comprehensive and applicable health care guidelines for common complex diseases in Koreans, reduce the burden of chronic diseases and improve the quality of life.

Cohort Profile: The Korean Genome and Epidemiology Study (KoGES) Consortium

It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a "Negrito" group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.

https://www.cell.com/ajhg/pdf/S0002-9297(11)00395-8.pdf

Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.

Tomohiro Koike

Papers

Mapping human genetic diversity in Asia