Abstract：
:We address the task of genotype imputation to a dense reference panel given genotype likelihoods computed from ultralow coverage sequencing as inputs. In this setting, the data have a high-level of missingness or uncertainty, and are thus more amenable to a probabilistic representation. Most existing imputation algorithms are not well suited for this situation, as they rely on prephasing for computational efficiency, and, without definite genotype calls, the prephasing task becomes computationally expensive. We describe GeneImp, a program for genotype imputation that does not require prephasing and is computationally tractable for whole-genome imputation. GeneImp does not explicitly model recombination, instead it capitalizes on the existence of large reference panels-comprising thousands of reference haplotypes-and assumes that the reference haplotypes can adequately represent the target haplotypes over short regions unaltered. We validate GeneImp based on data from ultralow coverage sequencing (0.5×), and compare its performance to the most recent version of BEAGLE that can perform this task. We show that GeneImp achieves imputation quality very close to that of BEAGLE, using one to two orders of magnitude less time, without an increase in memory complexity. Therefore, GeneImp is the first practical choice for whole-genome imputation to a dense reference panel when prephasing cannot be applied, for instance, in datasets produced via ultralow coverage sequencing. A related future application for GeneImp is whole-genome imputation based on the off-target reads from deep whole-exome sequencing.
journal_name
Geneticsjournal_title
Geneticsauthors
Spiliopoulou A,Colombo M,Orchard P,Agakov F,McKeigue Pdoi
10.1534/genetics.117.200063subject
Has Abstractpub_date
2017-05-01 00:00:00pages
91-104issue
1eissn
0016-6731issn
1943-2631pii
genetics.117.200063journal_volume
206pub_type
杂志文章相关文献
GENETICS文献大全abstract：:The Acp26Aa and Acp26Ab genes that code for male accessory gland proteins are tandemly arranged in the species of the Drosophila melanogaster complex. An approximately 1.6-kb region encompassing both genes has been sequenced in 10, 24, and 18 lines from Spain, Ivory Coast, and Malawi, respectively; the previously stud...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1998-11-01 00:00:00
abstract：:We have created a resource to rapidly map genetic traits to specific chromosomes in yeast. This mapping is done using a set of 16 yeast strains each containing a different chromosome with a conditionally functional centromere. Conditional centromere function is achieved by integration of a GAL1 promoter in cis to cent...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.108.087999
更新日期：2008-12-01 00:00:00
abstract：:Grain yield is a major goal for the improvement of durum wheat, particularly in drought-prone areas. In this study, the genetic basis of grain yield (GY), heading date (HD), and plant height (PH) was investigated in a durum wheat population of 249 recombinant inbred lines evaluated in 16 environments (10 rainfed and 6...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.107.077297
更新日期：2008-01-01 00:00:00
abstract：:The evolution of domesticated maize from its wild ancestor teosinte is a dramatic example of the effect of human selection on agricultural crops. Maize has one dominant axis of growth, whereas teosinte is highly branched. The axillary branches in maize are short and feminized whereas the axillary branches of teosinte ...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2002-12-01 00:00:00
abstract：:A system for genetic analysis in the cellular slime mold P. violaceum has been developed. Two growth-temperature-sensitive mutants were isolated in a haploid strain and used to select rare diploid heterozygotes arising by spontaneous fusion of the haploid cells. A recessive mutation to cycloheximide resistance in one ...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1976-05-01 00:00:00
abstract：:Several eukaryotic homologs of the Escherichia coli RecQ DNA helicase have been found. These include the human BLM gene, whose mutation results in Bloom syndrome, and the human WRN gene, whose mutation leads to Werner syndrome resembling premature aging. We cloned a Drosophila melanogaster homolog of the RECQ helicase...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1999-03-01 00:00:00
abstract：:Animal microRNAs (miRNA) are implicated in the control of nearly all cellular functions. Due to high sequence redundancy within the miRNA gene pool, loss of most of these 21- to 24-bp long RNAs individually does not cause a phenotype. Thus, only very few miRNAs have been associated with clear functional roles. We cons...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.112.145383
更新日期：2012-12-01 00:00:00
abstract：:The genetic effects of one generation of spermatogonial X-irradiation in rats, by a single dose of 600r in one experiment and by a fractionated dose of 450r in another, were measured in three generations of their descendants. Estimates of dominant lethal mutation rates--(2 to 3) X 10-4/gamete/r--from litter size diffe...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1977-02-01 00:00:00
abstract：:Bacteriophage T4 DNA metabolism is largely insulated from that of its host, although some host functions assist in the repair of T4 DNA damage. Environmental factors sometimes affect survival and mutagenesis after ultraviolet (UV) irradiation of T4, and can affect mutagenesis in many organisms. We therefore tested the...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1998-04-01 00:00:00
abstract：:We have investigated meiotic changes in CAG repeat tracts embedded in a yeast chromosome. Repeat tracts undergo either conversion events between homologs or expansion and contraction events that appear to be confined to a single chromatid. We did not find evidence for conversion of tract interruptions or excess exchan...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2001-12-01 00:00:00
abstract：:We formalize the use of allele frequency and geographic information for the construction of gene trees at the intraspecific level and extend the concept of evolutionary parsimony to molecular variance parsimony. The central principle is to consider a particular gene tree as a variable to be optimized in the estimation...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1994-01-01 00:00:00
abstract：:Using conditional probabilities and moment-generating matrices, I derived approximate algebraic equations that give expectations of gene frequency, population mean, gene frequency variance within lines, or heterozygosity, and gene frequency variance between lines, or drift, for repeated cycles of recurrent selection i...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1980-07-01 00:00:00
abstract：:Mutations that confer the loss of a single biochemical property (separation-of-function mutations) can often uncover a previously unknown role for a protein in a particular biological process. However, most mutations are identified based on loss-of-function phenotypes, which cannot differentiate between separation-of-...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.112.147801
更新日期：2013-03-01 00:00:00
abstract：:The hitchhiking model of population genetics predicts that an allele favored by Darwinian selection can replace haplotypes from the same locus previously established at a neutral mutation-drift equilibrium. This process, known as "selective sweep," was studied by comparing molecular variation between the polymorphic I...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1999-07-01 00:00:00
abstract：:The opportunistic human pathogen Penicillium marneffei exhibits a temperature-dependent dimorphic switch. At 25 degrees, multinucleate, septate hyphae that can undergo differentiation to produce asexual spores (conidia) are produced. At 37 degrees hyphae undergo arthroconidiation to produce uninucleate yeast cells tha...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2003-06-01 00:00:00
abstract：:Population structure parameters commonly used for diploid species are reexamined for the particular case of tetrasomic inheritance (autotetraploid species). Recurrence equations that describe the evolution of identity probabilities for neutral genes in an "island model" of population structure are derived assuming tet...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1998-10-01 00:00:00
abstract：:Knowledge of multigenic family organization should provide insight into their mode of evolution. Accordingly, we characterized the 5S ribosomal gene family in the Drosophila melanogaster strain ry506. The 5S genes in this strain display a striking HindIII restriction difference compared to the "standard" D. melanogast...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1988-04-01 00:00:00
abstract：:Yeast cells deficient in the transcriptional activator Imp2p are viable, but display marked hypersensitivity to a variety of oxidative agents. We now report that imp2 null mutants are also extremely sensitive to elevated levels of the monovalent ions, Na+ and Li+, as well as to the divalent ions Ca2+, Mn2+, Zn2+, and ...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1998-06-01 00:00:00
abstract：:We identified the Drosophila melanogaster Signal peptide peptidase gene (Spp) that encodes a multipass transmembrane aspartyl protease. Drosophila SPP is homologous to the human signal peptide peptidase (SPP) and is distantly related to the presenilins. We show that, like human SPP, Drosophila SPP can proteolyze a mod...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.104.039933
更新日期：2005-05-01 00:00:00
abstract：:Cyclic guanosine monophosphate (cGMP) is a key secondary messenger used in signal transduction in various types of sensory neurons. The importance of cGMP in the ASE gustatory receptor neurons of the nematode Caenorhabditis elegans was deduced by the observation that multiple receptor-type guanylyl cyclases (rGCs), en...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.113.152660
更新日期：2013-08-01 00:00:00
abstract：:Cornell Control White Leghorn chicks were grown in a common environment to five weeks of age and selected for fast and slow gain in body weight from five to nine weeks of age at two temperatures, 21.1 degrees (cold) and 32.2 degrees (hot), during which time a constant 50% relative humidity was maintained. All lines we...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1981-02-01 00:00:00
abstract：:The process of close recombinant formation in bacteriophage T5 crosses has been studied by examining the structure of internal heterozygotes (HETs), the immediate products of recombination events. The T5 system was chosen because it permits the study of internal heterozygotes exclusively, thus avoiding the ambiguities...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1980-09-01 00:00:00
abstract：:Distributive disjunction is defined as the first division meiotic segregation of either nonhomologous chromosomes that lack homologs or homologous chromosomes that have not recombined. To determine if chromosomes from the yeast Saccharomyces cerevisiae were capable of distributive disjunction, we constructed a strain ...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1991-03-01 00:00:00
abstract：:For more than 60 years, evolutionary cytogeneticists have been using naturally occurring chromosomal inversions to infer phylogenetic histories, especially in insects with polytene chromosomes. The validity of this method is predicated on the assumption that inversions arise only once in the history of a lineage, so t...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1998-10-01 00:00:00
abstract：:Two composite multiple regression-interval mapping analyses were performed to identify candidate quantitative trait loci (QTL) affecting components of wing shape in Drosophila melanogaster defined by eight relative warp-based measures. A recombinant inbred line design was used to map QTL for the shape of two intervein...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2000-06-01 00:00:00
abstract：:A common theme in medical microbiology is that the amount of amino acid sequence variation in proteins that are targets of the host immune system greatly exceeds that found in metabolic enzymes or other housekeeping proteins. Twenty-four Mycobacterium tuberculosis genes coding for targets of the host immune system wer...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2000-05-01 00:00:00
abstract：:The small ovary gene (sov) is required for the development of the Drosophila ovary. Six EMS-induced recessive alleles have been identified. Hypomorphic alleles are female sterile and have no effect on male fertility, whereas more severe mutations result in lethality. The female-sterile alleles produce a range of mutan...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1995-03-01 00:00:00
abstract：:The forest tent caterpillar is polymorphic for two melanic genes affecting wing color of moths. These are the first genetically determined morphological traits reported for the genus. Dark (D) is a sex-limited, autosomal dominant with a phenotype of dark brown males. Frequencies in population samples varied from 8 to ...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1979-06-01 00:00:00
abstract：:The percentage of crossovers is consistently higher in plants hypoploid for six B-A translocations when crossed as males than when crossed as females; in most instances, this excess of male crossing over exceeds that found in control crosses (involving normal chromosomes). Thus, there seems to be something about the h...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1984-05-01 00:00:00
abstract：:Nucleostemin 3 (NS3) is an evolutionarily conserved protein with profound roles in cell growth and viability. Here we analyze cell-autonomous and non-cell-autonomous growth control roles of NS3 in Drosophila and demonstrate its GTPase activity using genetic and biochemical assays. Two null alleles of ns3, and RNAi, de...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.112.149104
更新日期：2013-05-01 00:00:00
