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1 SNV patterns resembled those found in cancer cell genome
2 SNV RNA levels were higher in the lungs but not differen
3 SNVs with a frequency of >2% in brain were also present
4 -specific variant panels, which covers 99.0% SNVs of minor allele frequency >/=0.1%, and its value fo
5 were considered reinfection, and those 3-10 SNVs apart (or without whole-genome sequences) were cons
6 were considered relapses, paired samples >10 SNVs apart were considered reinfection, and those 3-10 S
7 c diversity of isolates was between 0 and 15 SNVs during the outbreak; molecular clock calculations e
14 ndividual with multisite colonization was 41 SNVs, with no systematic divergence among body sites.
18 resholds differed between 129S-Cdh23(c.753A) SNV and 129S1.B6-Cdh23(ahl) congenic mice, and a linkage
19 mutation rate of approximately 1.5 x 10(-8) SNVs per site per generation with a significantly higher
21 of 51,138 protein functional site affecting SNVs (pfsSNVs), a pan-cancer analysis revealed 142 somat
22 olyclonal antibody administered 5 days after SNV infection conferred significant protection against d
23 s an effort to collect, classify and analyze SNVs that may affect the optimal response to currently a
26 the mutational signatures, copy number, and SNV mutational profiles reflect the expected heterogenei
27 Probands carry more gene-disruptive CNVs and SNVs, resulting in severe missense mutations and mapping
29 he batch effect, virus expression level, and SNVs as part of next-generation sequencing (NGS) data an
31 vide valuable benchmark for state-of-the-art SNV calling methods, but also shed light on the access t
32 potentially independent novel BP-associated SNV, rs3416322 (missense, SYNPO2L) at a known locus, unc
33 eal a novel mechanism for disease-associated SNVs and provide a platform for modeling morphological c
38 showed that the deleteriousness of autosomal SNVs was significantly higher in female probands (p = 0.
39 stitute of Standards and Technology for both SNVs (>99.99%) and indels (99.92%) and add a validated t
43 a stringent GATK-based pipeline for calling SNVs including SNPs and RNA editing events in RNA-seq re
46 ), a tool to score both noncoding and coding SNVs based on their potential to regulate the expression
47 e identified less-common and rare non-coding SNVs associated with BMD independently from GWAS common
49 n interactions on deleterious protein-coding SNVs; and identify pathways and networks that have likel
50 -of-function effects of multiple rare coding SNVs found in SCZ subjects in the GIT1 (G protein-couple
51 The estimated mean number of real coding SNVs (656 variants, approximately 3% of all coding HQ SN
54 analysis identifies potentially deleterious SNVs present on drug-binding residues that are relevant
55 mic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mito
56 biological data, SiNVICT was able to detect SNVs and indels with variant allele percentages as low a
57 ct and quantify SNVs in the RNA and discover SNVs with altered frequencies between distinct cellular
58 ttings, RNA2DNAlign identified 2038 distinct SNV sites associated with one of the aforementioned asym
65 ve (AUC) of 0.807, and discriminate cis-eQTL SNVs shared across six populations of different ancestry
66 res discriminate cis-eQTL SNVs from non-eQTL SNVs in the training set with a cross-validated area und
70 the AUROCs were lower (0.86 for SE; 0.80 for SNV) when data for all individuals were included, they r
76 Although there are additional values for SNVs detection, the assembly-based approach would have g
78 factor motif, except the more than 100 GMAS SNVs in linkage disequilibrium with polymorphisms report
81 identified exclusively by WES whereas 692 HQ SNVs and 105 indels were identified exclusively by WGS.
83 variants, approximately 3% of all coding HQ SNVs) identified by WGS and missed by WES was greater th
84 , a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called by both pla
87 nst rapid fibrosis progression for the IL28B SNV (G allele), MLEC SNV (T allele), and DDX5 SNV (G all
90 titution sequencing errors not only improves SNV call precision at low mapping quality regions, but a
92 heetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC cl
93 extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II ge
94 elvaraj et al demonstrated single individual SNV phasing is possible with proximity ligated (HiC) seq
95 Methods to predict whether or not individual SNVs are likely to regulate gene expression would aid in
98 les here demonstrate that even if the mapped SNVs predicted as deleterious may not result in signific
99 ly distinct subtypes were identified (median SNV difference 273, IQR 162-399) at a rate of 38 (IQR 34
104 dence of an association at a novel, missense SNV, rs7739323, which is located in the ubiquitin protei
108 oplet digital PCR experiments confirmed more SNVs as mosaic with AF as low as 0.01%, suggesting that
116 gible numbers of false positive and negative SNV and INDEL calls that were shown to be enriched among
118 association of a low-frequency nonsynonymous SNV in GLP1R (A316T; rs10305492; MAF=1.4%) with lower FG
119 at the fraction of deleterious nonsynonymous SNVs is higher than previously reported; quantify the ef
120 at the fraction of deleterious nonsynonymous SNVs is significantly higher for Mendelian versus comple
122 SNPs and RNA editing sites as well as novel SNVs, with the majority of DVRs corresponding to known R
124 NV hits for genes impacted by autism de novo SNVs (P=0.019 for non-synonymous SNV genes) did not surv
125 otwithstanding this prescreening, 84 de novo SNVs affecting the coding region were identified, which
128 es with the most significantly associated NS SNVs, while regions associated with PD by a recent Genom
130 nor any gene carrying a higher burden of NS SNVs was significantly associated with PD status after m
133 human genome and compared the efficiency of SNV calling between the assembly-based and alignment-bas
134 ation and edema within the alveolar septa of SNV-infected hamsters, results which are similar to what
135 increases the sensitivity and specificity of SNV and indel detection at very low variant allele frequ
137 e genome datasets, ensemble joint calling of SNVs for low coverage data can be accomplished in a scal
140 igned specifically to predict the effects of SNVs on RNA structure, in particular remuRNA, RNAsnp and
142 missed by WES was greater than the number of SNVs identified by WES and missed by WGS (26 variants).
143 led no significant increase in the number of SNVs per cell, suggesting that a major fraction of mosai
144 disproportionately increases the numbers of SNVs in genes, rather than in nongenic regions of the ge
151 icipants, 30 of 4300 (0.7%) had a pathogenic SNV and six (0.1%) had a disruptive variant that was exp
152 cipants, six of 2203 (0.3%) had a pathogenic SNV and six (0.3%) had an expected pathogenic disruptive
157 hms designed to help identify and prioritize SNVs across the human genome for further investigation.
158 le up to over 10,000 samples while producing SNV callsets with high sensitivity and specificity.
159 fic perturbation, we can detect and quantify SNVs in the RNA and discover SNVs with altered frequenci
161 than non-disease related variants, and rare SNVs tend to disrupt local interactions to a larger exte
162 ts of 23 random forests trained to recognize SNVs in cis-expression quantitative trait loci (cis-eQTL
163 itive results: for instance, disease-related SNVs create stronger changes in localized frustration th
164 of short reads was needed to ensure reliable SNV calling and to generate assembled contigs with a goo
167 among a selection of popular multiple sample SNV callers, while showing exceptional recall in calling
168 e testing problem endemic to multiple sample SNV calling and utilizes high performance computing (HPC
169 iously published work with the single sample SNV caller genotype model selection (GeMS), a multiple s
174 Vs, we identified 17 loss of functional site SNVs and 60 gain of functional site SNVs which are signi
175 nal site SNVs and 60 gain of functional site SNVs which are significantly enriched in patients with s
179 R-TKI-resistant patients to identify somatic SNVs, small indels, CNVs and gene fusions in 508 tumor-r
181 Less obviously, we observe that somatic SNVs associated with oncogenes and tumor suppressor gene
182 ll as smaller de novo CNVs and exon-specific SNVs missed by exome sequencing in neurodevelopmental ge
184 UK Biobank, in whom 77 of the 100 suggestive SNVs were available for association analysis with systol
191 most types of protein functional sites, the SNV pattern differs between germline and somatic mutatio
192 Clinical significance of only 9.56% of the SNVs is known in ClinVar, although 79.02% are predicted
194 thresholds and cochlear pathologies of these SNV mice with those of congenic (B6.129S1-Cdh23(Ahl+) an
196 iched in tumor suppressors, and 97% of these SNVs generated a premature termination codon, leading to
197 iants (SNVs); however, the majority of these SNVs have unknown functional consequences, leaving their
200 We find that private, inherited truncating SNVs in conserved genes are enriched in probands (odds r
201 ssion model, we show that private truncating SNVs and rare, inherited CNVs are statistically independ
203 el phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient po
206 analyses for both single nucleotide variant (SNV) and copy number variant (CNV) alleles allowed for i
207 r popular somatic single nucleotide variant (SNV) calling methods (Varscan, SomaticSniper, Strelka an
208 riant callers for single nucleotide variant (SNV) calling, which leverages hybrid computing infrastru
209 orphism (SNP) and single-nucleotide variant (SNV) data, we see that genes with pathogenic expression-
210 tion of published single-nucleotide variant (SNV) de novo mutations showed evidence consistent with p
212 nstrate excellent single-nucleotide variant (SNV) detection using targeted sequencing of droplet MDA
213 o gene-disruptive single-nucleotide variant (SNV) had been detected by microarray or whole-exome sequ
214 number (CNV) and single nucleotide variant (SNV) in a small set of genes from individuals with epile
215 d reads that span single-nucleotide variant (SNV) loci and nearby splice junctions, assessing the co-
217 n-synonymous (NS) single nucleotide variant (SNV) nor any gene carrying a higher burden of NS SNVs wa
220 ctional inherited single-nucleotide variant (SNV) that accounts for several breast cancer risk-associ
221 detecting ASE on single nucleotide variant (SNV), exon and gene levels from sequencing data without
222 novel locus (lead single-nucleotide variant [SNV] rs12614435; p = 6.76 x 10(-18)) comprised intronic
223 have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be des
224 se nonsynonymous single-nucleotide variants (SNVs) across the whole genome of 216 neovascular AMD cas
225 enes, exons, and single-nucleotide variants (SNVs) all demonstrated positive selection or accelerated
226 nome has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events that result i
227 udes >59 million single-nucleotide variants (SNVs) and 9,212 private copy number variants (CNVs), of
228 ve set of exonic single-nucleotide variants (SNVs) and copy number variants (CNVs) from 2,377 familie
229 iants, including single-nucleotide variants (SNVs) and copy number variants (CNVs), in the non-coding
230 ate detection of single nucleotide variants (SNVs) and indels from cfDNA is constrained by several fa
231 analysis of SVs, single-nucleotide variants (SNVs) and short insertion/deletion (indel) variants from
232 mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected p
233 red samples </=2 single-nucleotide variants (SNVs) apart were considered relapses, paired samples >10
235 and validated 56 single nucleotide variants (SNVs) associated with BP from meta-analyses of exome chi
236 2 million novel, single-nucleotide variants (SNVs) at an estimated false discovery rate of <1.0%.
237 o non-synonymous single-nucleotide variants (SNVs) by conducting whole exome sequencing of 18 trios c
238 a gene can have single nucleotide variants (SNVs) due to single nucleotide polymorphisms (SNPs) in t
239 disease-causing single nucleotide variants (SNVs) from Human Gene Mutation Database and 10 002 putat
240 han 3 million of single nucleotide variants (SNVs) from the whole human genome and compared the effic
242 mately 1 million single nucleotide variants (SNVs) identified in high-coverage exome sequences of 651
243 nable pathogenic single-nucleotide variants (SNVs) in all 4300 European- and 2203 African-ancestry pa
244 entified somatic single-nucleotide variants (SNVs) in cancer, the extent to which these variants trig
247 s indicated that single nucleotide variants (SNVs) in the gene encoding the actin cytoskeletal regula
249 uence-disrupting single-nucleotide variants (SNVs) in these individuals compared with psychiatrically
250 which noncoding single nucleotide variants (SNVs) influence downstream phenotypes is through the reg
251 Discovering single-nucleotide variants (SNVs) is also of great importance for the identification
252 etection of rare single nucleotide variants (SNVs) is important for understanding genetic heterogenei
253 induced de novo single-nucleotide variants (SNVs) is strikingly different; with clustered mutations
254 threshold of 40 single-nucleotide variants (SNVs) or fewer to define subtypes and infer recent trans
255 g of 4.7 million single-nucleotide variants (SNVs) plus 0.7 million small (1-50 bp) insertions and de
256 (<1% frequency) single-nucleotide variants (SNVs) revealed that the gene encoding brain-derived neur
258 Identifying single nucleotide variants (SNVs) that contribute to differences in drug response an
259 o identify known single nucleotide variants (SNVs) using 6 control samples with publically available
260 kage for calling single nucleotide variants (SNVs) using NGS data from multiple same-patient samples.
261 per patient) and single-nucleotide variants (SNVs) were analyzed, with reference to the index patient
265 ith all possible single nucleotide variants (SNVs), and measure strong effects on transcript abundanc
266 ations including single-nucleotide variants (SNVs), chromosomal deletions, as well as integration of
269 iants, including single nucleotide variants (SNVs), in glutamatergic synaptic genes are enriched in s
270 the detection of single nucleotide variants (SNVs), information on copy number variants (CNVs) is of
272 o high frequency single nucleotide variants (SNVs), rs11544484 (V256I, Minor Allele Frequency = 0.27)
274 yses has been on single nucleotide variants (SNVs), with the contribution of small insertions and del
282 covered numerous single-nucleotide variants (SNVs); however, the majority of these SNVs have unknown
283 o non-synonymous single-nucleotide variants (SNVs; P=5.4 x 10(-4)) and targets of the Fragile X menta
285 rsity (mean 17.5 single nucleotide variants [SNVs] [95% confidence interval {CI}, 17.3 to 17.8]) comp
286 cond derivative and standard normal variate (SNV) transformation pre-treatments were applied to class
287 based on human single nucleotide variation (SNV) analysis of two separate HeLa cell lines and severa
288 traint based on single-nucleotide variation (SNV) and was independently correlated with measures of e
289 ovides reliable single-nucleotide variation (SNV) detection across the single-cell genome, facilitati
290 r, identifying single-nucleotide variations (SNVs) can be accomplished by sequencing kindred cells.
293 same 10 novel single nucleotide variations (SNVs), leading us to hypothesize that one patient was in
294 den of somatic single-nucleotide variations (SNVs), with each case containing a TERT promoter (TERT-p
295 of NP (NPcore) encoded by Sin Nombre virus (SNV) and Andes virus (ANDV), which are two representativ
296 and fluorescently labeled Sin Nombre virus (SNV) to the integrin PSI domain stimulates higher affini
297 the natural reservoirs of Sin Nombre virus (SNV), the etiologic agent of most HCPS cases in North Am
298 total DNA used for the biological data where SNVs and indels could be detected with very high sensiti
299 cyclophosphamide, followed by infection with SNV, results in a vascular leak syndrome that accurately
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