RefSeq: an update on mammalian reference sequences

Pruitt, Kim D.; Brown, Garth; Hiatt, Susan M.; Thibaud‐Nissen, Françoise; Astashyn, Alexander; Ermolaeva, Olga; Farrell, Catherine; Hart, Jennifer; Landrum, Melissa; McGarvey, Kelly M.; Murphy, Michael R.; O’Leary, Nuala; Pujar, Shashikant; Rajput, Bhanu; Rangwala, Sanjida H; Riddick, Lillian D.; Shkeda, Andrei; Sun, Hanzhen; Tamez, Pamela A.; Tully, Raymond E.; Wallin, Craig; Webb, David; Weber, Janet A.; Wu, Wendy; DiCuccio, Michael; Kitts, Paul; Maglott, Donna; Murphy, Terence; Ostell, James

doi:10.1093/nar/gkt1114

Cited by 897 publications

(836 citation statements)

References 24 publications

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“…iberiensis and C‐lineage individuals using the training data set. To uncover the putative functional role of the highly differentiated SNPs, we used SNPeff 4.3 (Cingolani et al., 2012) and the NCBI honeybee annotation version 102 (Pruitt et al., 2013). Subsequently, we performed a gene ontology (GO) analysis in the DAVID v.8.0 database (Huang, Sherman, & Lempicki, 2009) considering the GO terms of the biological process (BP), molecular function (MF), cellular component (CC) (Gene Ontology Consortium, 2015) and the KEGG pathway (Kanehisa, Sato, Kawashima, Furumichi, & Tanabe, 2016).…”

Section: Methodsmentioning

confidence: 99%

Developing reduced SNP assays from whole‐genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

Henriques

Parejo

Vignal

et al. 2018

Evolutionary Applications

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The most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In western Europe, one such threat is large‐scale introductions of commercial strains (C‐lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M‐lineage ancestry). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C‐lineage introgression in the most diverse and evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis mellifera iberiensis). We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (FST = 1) is introduced when the sample size is small (N ≤ 10) and when sampling only captures a small fraction of a population's genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training data set to design four independent SNP assays selected from pairwise FST between the Iberian and C‐lineage honeybees. The designed assays, which were validated in holdout and simulated hybrid data sets, proved to be highly accurate and can be readily used for monitoring populations not only in the native range of A. m. iberiensis in Iberia but also in the introduced range in the Balearic islands, Macaronesia and South America, in a time‐ and cost‐effective manner. While our approach used the Iberian honeybee as model system, it has a high value in a wide range of scenarios for the monitoring and conservation of potentially hybridized domestic and wildlife populations.

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Section: Methodsmentioning

confidence: 99%

Developing reduced SNP assays from whole‐genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

Henriques

Parejo

Vignal

et al. 2018

Evolutionary Applications

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“…Variant information was gathered from population databases (Exome Aggregation Consortium 14 , Exome Variant server 15 , 1000 Genomes 16 , dbSNP 17 and dbVAR 18 ), disease databases (humsavar.txt release 2016_05 19 , ClinVar 20 , HGMD-public 21 , OMIM 22 and OMIA 23 ) and sequence databases (RefSeqGene 24 , NCBI Genome 25 , UCSC Genome 26 and Ensembl Genome 27 ). I-Mutant2.0 28 was used as a predictor of protein stability changes upon variations.…”

Section: Bioinformatics Tools For Sequence Variant Interpretationmentioning

confidence: 99%

The novel homozygous KCNJ10 c.986T>C (p.(Leu329Pro)) variant is pathogenic for the SeSAME/EAST homologue in Malinois dogs

et al. 2016

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SeSAME/EAST syndrome is a multisystemic disorder in humans, characterised by seizures, sensorineural deafness, ataxia, developmental delay and electrolyte imbalance. It is exclusively caused by homozygous or compound heterozygous variations in the KCNJ10 gene. Here we describe a similar syndrome in two families belonging to the Malinois dog breed, based on clinical, neurological, electrodiagnostic and histopathological examination. Genetic analysis detected a novel pathogenic KCNJ10 c.986T4C (p.(Leu329Pro)) variant that is inherited in an autosomal recessive way. This variant has an allele frequency of 2.9% in the Belgian Malinois population, but is not found in closely related dog breeds or in dog breeds where similar symptoms have been already described. The canine phenotype is remarkably similar to humans, including ataxia and seizures. In addition, in half of the dogs clinical and electrophysiological signs of neuromyotonia were observed. Because there is currently no cure and treatment is nonspecific and unsatisfactory, this canine translational model could be used for further elucidating the genotype/ phenotype correlation of this monogenic multisystem disorder and as an excellent intermediate step for drug safety testing and efficacy evaluations before initiating human studies.

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“…30 When the nucleotide position is indicated, the GenBank cDNA reference sequences were used as follows: AIPL1 (NG_008474.1); CEP290 (NG_008417.1); CRB1 (NG_008483.1); GUCY2D (NG_009092.1); LRAT (NG_009110.1); RDH12 (NG_008321.1); RPE65 (NG_008472.1); RPGRIP1 (NG_008933.1); and TULP1 (NG_009077.1). 31 …”

Section: Sequence Variants Nomenclaturementioning

confidence: 99%

Comprehensive genotyping reveals RPE65 as the most frequently mutated gene in Leber congenital amaurosis in Denmark

et al. 2015

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Leber congenital amaurosis (LCA) represents the most severe form of inherited retinal dystrophies with an onset during the first year of life. Currently, 21 genes are known to be associated with LCA and recurrent mutations have been observed in AIPL1, CEP290, CRB1 and GUCY2D. In addition, sequence analysis of LRAT and RPE65 may be important in view of treatments that are emerging for patients carrying variants in these genes. Screening of the aforementioned variants and genes was performed in 64 Danish LCA probands. Upon the identification of heterozygous variants, Sanger sequencing was performed of the relevant genes to identify the second allele. In combination with prior arrayed primer extension analysis, this led to the identification of two variants in 42 of 86 cases (49%). Remarkably, biallelic RPE65 variants were identified in 16% of the cases, and one novel variant, p.(D110G), was found in seven RPE65 alleles. We also collected all previously published RPE65 variants, identified in 914 alleles of 539 patients with LCA or early-onset retinitis pigmentosa, and deposited them in the RPE65 Leiden Open Variation Database (LOVD). The in silico pathogenicity assessment of the missense and noncanonical splice site variants, as well as an analysis of their frequency in~60 000 control individuals, rendered 864 of the alleles to affect function or probably affect function. This comprehensive database can now be used to select patients eligible for gene augmentation or retinoid supplementation therapies.

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RefSeq: an update on mammalian reference sequences

Cited by 897 publications

References 24 publications

Developing reduced SNP assays from whole‐genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

Developing reduced SNP assays from whole‐genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

The novel homozygous KCNJ10 c.986T>C (p.(Leu329Pro)) variant is pathogenic for the SeSAME/EAST homologue in Malinois dogs

Comprehensive genotyping reveals RPE65 as the most frequently mutated gene in Leber congenital amaurosis in Denmark

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