Exome sequencing of 118 patients with neurodevelopmental disorders shows that this technique is useful for identifying new pathogenic mutations and for correcting diagnosis in ~10% of cases.

Through long-term laboratory selection (over 200 generations), we have generated Drosophila melanogaster populations that tolerate severe, normally lethal, levels of hypoxia. Because of initial experiments suspecting genetic mechanisms underlying this adaptation, we compared the genomes of the hypoxia-selected flies with those of controls using deep resequencing. By applying unique computing and analytical methods we identified a number of DNA regions under selection, mostly on the X chromosome. Several of the hypoxia-selected regions contained genes encoding or regulating the Notch pathway. In addition, previous expression profiling revealed an activation of the Notch pathway in the hypoxia-selected flies. We confirmed the contribution of Notch activation to hypoxia tolerance using a specific γ-secretase inhibitor, N-[N-(3,5-Difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT), which significantly reduced adult survival and life span in the hypoxiaselected flies. We also demonstrated that flies with loss-of-function Notch mutations or RNAi-mediated Notch knockdown had a significant reduction in hypoxia tolerance, but those with a gain-of-function had a dramatic opposite effect. Using the UAS-Gal4 system, we also showed that specific overexpression of the Notch intracellular domain in glial cells was critical for conferring hypoxia tolerance. Unique analytical tools and genetic and bioinformatic strategies allowed us to discover that Notch activation plays a major role in this hypoxia tolerance in Drosophila melanogaster.evolution | next-generation sequencing O xygen homoeostasis is essential for development, growth, and integrity of cells, tissues, and organisms. Limited oxygen supply to cells and tissues (hypoxia) has a wide range of physiologic and potentially pathologic consequences, ranging from ischemic/hypoxic heart disease, stroke, and pulmonary hypertension to a number of obstetrical/perinatal complications, to high-altitude illnesses, to organ transplantation, and finally to intratumor hypoxia and cancer progression. Despite the clinical importance and societal disease impact of such a wide range of disorders, the molecular underpinnings of susceptibility or tolerance of cells or tissues to lack of O 2 are not well understood. Many studies have investigated the mechanisms that lead to injury when cells are deprived of O 2 , but to potentially treat or prevent the consequences of hypoxia necessitates also the understanding of the inherent tissue mechanisms that are critical for tolerance and survival. To do so, we use a long-term laboratory selection strategy that unmasks mechanisms that play an important role in hypoxia tolerance in a genetic model, Drosophila melanogaster (1, 2). In this attempt, starting with 27 isofemale D. melanogaster strains, and applying decreasing levels of O 2 over >200 generations, we generated Drosophila populations that tolerate severe levels of hypoxia, which are lethal to the original parental lines. These hypoxia-adapted flies (AF) pass the tolerance trait ...

The hypoxic conditions at high altitudes present a challenge for survival, causing pressure for adaptation. Interestingly, many high-altitude denizens (particularly in the Andes) are maladapted, with a condition known as chronic mountain sickness (CMS) or Monge disease. To decode the genetic basis of this disease, we sequenced and compared the whole genomes of 20 Andean subjects (10 with CMS and 10 without). We discovered 11 regions genome-wide with significant differences in haplotype frequencies consistent with selective sweeps. In these regions, two genes (an erythropoiesis regulator, SENP1, and an oncogene, ANP32D) had a higher transcriptional response to hypoxia in individuals with CMS relative to those without. We further found that downregulating the orthologs of these genes in flies dramatically enhanced survival rates under hypoxia, demonstrating that suppression of SENP1 and ANP32D plays an essential role in hypoxia tolerance. Our study provides an unbiased framework to identify and validate the genetic basis of adaptation to high altitudes and identifies potentially targetable mechanisms for CMS treatment.

Genetic adaptation to external stimuli occurs through the combined action of mutation and selection. A central problem in genetics is to identify loci responsive to specific selective constraints. Many tests have been proposed to identify the genomic signatures of natural selection by quantifying the skew in the site frequency spectrum (SFS) under selection relative to neutrality. We build upon recent work that connects many of these tests under a common framework, by describing how selective sweeps affect the scaled SFS. We show that the specific skew depends on many attributes of the sweep, including the selection coefficient and the time under selection. Using supervised learning on extensive simulated data, we characterize the features of the scaled SFS that best separate different types of selective sweeps from neutrality. We develop a test, SFselect, that consistently outperforms many existing tests over a wide range of selective sweeps. We apply SFselect to polymorphism data from a laboratory evolution experiment of Drosophila melanogaster adapted to hypoxia and identify loci that strengthen the role of the Notch pathway in hypoxia tolerance, but were missed by previous approaches. We further apply our test to human data and identify regions that are in agreement with earlier studies, as well as many novel regions. N ATURAL selection works by preferentially favoring carriers of beneficial (fit) alleles. At the genetic level, the increased fitness may stem from two sources: either a de novo mutation that is beneficial in the current environment or new environmental stress leading to increased relative fitness of an existing allele. Over time, haplotypes carrying such variants start to dominate the population, causing reduced genetic diversity. This process, known as a selective sweep, is mitigated by recombination and can therefore be observed mostly in the vicinity of the beneficial allele. Improving our ability to detect the genomic signatures of selection is crucial for shedding light on genes responsible for adaptation to environmental stress, including disease.Many tests of neutrality have been proposed based on the site frequency spectrum (Tajima 1989;Fay and Wu 2000;Zeng et al. 2006;Chen et al. 2010;Udpa et al. 2011). We start by describing these tests in a common framework delineated by Achaz (2009). The data, namely genetic variants from a population sample, is typically represented as a matrix with m columns corresponding to segregating sites, and n rows corresponding to individual chromosomes. The sample is chosen from a much larger population of N diploid individuals, where chromosomes are connected by a (hidden) genealogy and mutations occurring in a certain lineage are inherited by all of its descendants ( Figure 1A). Thus, in the example shown in Figure 1A, the mutation at locus 4 appears in four chromosomes from the sample, or 0.5 frequency. Following Fu (1995), let j i denote the number of polymorphic sites at frequency i/n in a sample of size n. The site frequency spectrum (SFS) ...

BackgroundAlthough it has long been proposed that genetic factors contribute to adaptation to high altitude, such factors remain largely unverified. Recent advances in high-throughput sequencing have made it feasible to analyze genome-wide patterns of genetic variation in human populations. Since traditionally such studies surveyed only a small fraction of the genome, interpretation of the results was limited.ResultsWe report here the results of the first whole genome resequencing-based analysis identifying genes that likely modulate high altitude adaptation in native Ethiopians residing at 3,500 m above sea level on Bale Plateau or Chennek field in Ethiopia. Using cross-population tests of selection, we identify regions with a significant loss of diversity, indicative of a selective sweep. We focus on a 208 kbp gene-rich region on chromosome 19, which is significant in both of the Ethiopian subpopulations sampled. This region contains eight protein-coding genes and spans 135 SNPs. To elucidate its potential role in hypoxia tolerance, we experimentally tested whether individual genes from the region affect hypoxia tolerance in Drosophila. Three genes significantly impact survival rates in low oxygen: cic, an ortholog of human CIC, Hsl, an ortholog of human LIPE, and Paf-AHα, an ortholog of human PAFAH1B3.ConclusionsOur study reveals evolutionarily conserved genes that modulate hypoxia tolerance. In addition, we show that many of our results would likely be unattainable using data from exome sequencing or microarray studies. This highlights the importance of whole genome sequencing for investigating adaptation by natural selection.