INDEL Mutation

Point Mutation

Mutation, Missense

Indel

Frameshift mutation

Gap penalty

January-March 2022 in science

Surveyor nuclease assay

Multiple sequence alignment

Intermediate filament

Desmin

Insertion (genetics)

KCNQ2 developmental and epileptic encephalopathy

Isozyme

ANNOVAR

1000 Genomes Project

Margaret Oakley Dayhoff

Comprehensive Antibiotic Resistance Database

Mutational signatures

Prime editing

DNA mismatch repair

List of RNA-Seq bioinformatics tools

Duplex sequencing

Library (biology)

Pseudogene

LDL receptor

CRISPR

Sequence alignment

Von Hippel-Lindau disease

Designer baby

Magnus von Knebel Doeberitz

Nucleic acid sequence

MutationTaster

SNPs5

• https://www.ebi.ac.uk/eva/) is a resource for sharing all types of genetic variation data (SNPs, indels, and structural variants) for all species. (nih.gov)
• annotate SNPs (finding SNPs and InDels that cause frame-shifts, missense mutations, etc. (jcvi.org)
• NGS's single-nucleotide resolution also enables it to detect even the smallest possible mutations (SNPs) without necessarily requiring knowledge of the mutation in advance. (aacc.org)
• Comprehensive, all-in-one detection of genome-wide CNVs, copy-neutral LOH (cnLOH), SNPs, and indels in one target enrichment capture. (agilent.com)
• We can help researchers identify SNPs, indels, gene copy numbers, and genomic rearrangements from the various types of DNA-sequencing and microarray data and provide tailored downstream analysis of variants and mutations. (nottingham.ac.uk)

Genes16

• Genetic mutations of FUT1 and FUT2 genes were analysed by DNA sequencing. (nih.gov)
• Blood samples from 331 randomly-selected Chinese donors were analysed with the SNaPshot system to distinguish five known mutations (Se C357T, A385T, G428A, G716A and FUT1 880delTT) in the FUT1 and FUT2 genes. (nih.gov)
• Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5' region of TP53, in the 3' untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. (lu.se)
• We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available. (lu.se)
• To report potentially pathogenic mutations in the keratin 3 ( KRT3 ) and keratin 12 ( KRT12 ) genes in two individuals with clinically diagnosed Meesmann corneal dystrophy (MECD). (molvis.org)
• If laboratories use NGS panels to detect or confirm mutations in specific genes, and are unlikely to expand their test repertoire, a fixed scope of accreditation is likely to be the most appropriate option. (ukas.com)
• If laboratories are using NGS panels more broadly, and wish to detect mutations in any of the genes covered by an NGS panel, add targets to a custom panel or add target types (e.g. fusion genes, CNVs, tandem repeats), a flexible scope of accreditation may be a suitable option. (ukas.com)
• Sanger sequencing may be used to detect specific or denovo mutations in specific genes using commercially sourced primers or in-house designed primers (manufactured outside of the accredited laboratory). (ukas.com)
• To identify mutations in COL2A1 and COL11A1 genes and to examine the genotype-phenotype correlation in a cohort of Chinese patients with Stickler syndrome. (molvis.org)
• Types 1 and 2 are caused by mutations in the COL2A1 (OMIM 120140 ) and COL11A1 (OMIM 120280 ) genes, respectively. (molvis.org)
• It is estimated that these two genes are responsible for more than 95% of the mutations in patients with Stickler syndrome ( HGMD , last updated in March 2015). (molvis.org)
• We also observed somatic mutations in multiple therapeutically relevant genes, which may represent candidate drug targets in this highly lethal tumor type. (biomedcentral.com)
• The team first compared coverage performance in what it described as the "medically interpretable genome" - a list of 5,419 genes in which mutations are known to cause disease or disease-related drug response. (genomeweb.com)
• In this study, by targeted next-generation sequencing of 414 known deafness genes, we identified compound heterozygous mutations p.R34X/p.M413T in TMC1 and p.S3417del/p.R1407T in MYO15A in two recessive Chinese Han deaf families. (hindawi.com)
• Using targeted next-generation sequencing of 414 known deafness genes, we identified compound heterozygous mutations in TMC1 and MYO15A as the genetic causes of the hearing loss in those families. (hindawi.com)
• We demonstrate that RNA‐seq can be used to call mutations in genes such as PIK3CA, TP53, and ERBB2, as well as the status of molecular pathways and mutational burden, and identify potentially druggable mutations in 86.8% of tumors. (lu.se)

Gene mutations3

• As corneal keratins naturally occur as obligate K3/K12 heterodimers, gene mutations altering the encoded protein of either KRT3 or KRT12 are expected to negatively impact the K3/K12 heterodimer complex. (molvis.org)
• NGS panels may detect numerous gene mutations. (ukas.com)
• Advances in sequencing technologies may allow for more efficient diagnosis of disease by combining analyses of phenotypes and gene mutations. (molvis.org)

Variants7

• Indels ≥ 50 bases in length are classified as structural variants. (wikipedia.org)
• Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). (lu.se)
• Genome assembly, annotation and variant analysis - Our team are proficient in dealing with whole genome, whole-exome and targeted sequencing methods that allow for the study of genetic variants or mutations. (nottingham.ac.uk)
• We are developing single-cell genome sequencing technologies to enable the discovery of the entire spectrum of DNA mutation -including the acquisition of ploidy changes, aneuploidies, copy number variants, structural variants, retrotranspositions, indels, and single nucleotide variants. (sanger.ac.uk)
• Wuhan strain will continue to arise, yet not all viral variants generated through mutation of the virus are important or have immediate public health relevance. (who.int)
• However, variants with specific mutations that affect the way the virus behaves are now considered either Variants of Interest (VOI) or Variants of Concern (VOC) with respect to public health implications (1). (who.int)
• Gene variants (also known as mutations) can have varying effects --on health, depending on where they occur and whether they alter the function of essential proteins. (medlineplus.gov)

Somatic4

• In addition, primary and metastatic tumor pairs were also likely to share somatic SNVs and small indels. (genomeweb.com)
• When bulk tumor tissues are profiled for somatic copy number alterations (sCNA) and point mutations, it may be difficult to estimate their cellular fractions when a mutation falls within a sCNA. (biomedcentral.com)
• The "cancer add-on" expands the tool to interpret somatic mutations according to AMP guidelines. (bio-itworld.com)
• Breast cancer is a disease of genomic alterations, of which the panorama of somatic mutations and how these relate to subtypes and therapy response is incompletely understood. (lu.se)

Heterozygous5

• A novel FOXL2 heterozygous indel mutation, c.19_95del, a 77-bp deletion that disrupts FOXL2 protein structure, was identified in all affected members of the family. (ijbs.com)
• Heterozygous mutations of FUT1 were identified by TOPO cloning sequencing. (nih.gov)
• Also, were the mutations homozygous or heterozygous, as C. albicans is an obligate diploid? (peerj.com)
• Heterozygous mutations would have left 50% cut / 50% uncut on the gel. (peerj.com)
• Asn102Ser) mutation in the heterozygous state. (biomedcentral.com)

Genetic5

• Indels, being either insertions, or deletions, can be used as genetic markers in natural populations, especially in phylogenetic studies. (wikipedia.org)
• While the most common mutation was in TP53 , the OTSCC genetic landscape differed from previously described cohorts of patients with head and neck tumors: OTSCCs demonstrated frequent mutations in DST and RNF213 , while alterations in CDKN2A and NOTCH1 were significantly less frequent. (biomedcentral.com)
• Standard methods sequence DNA that has been extracted from a population of cells, such that not only the genetic composition of individual cells is lost, but also de novo mutations in cell(s) are effectively concealed by the bulk signal. (sanger.ac.uk)
• Our study expanded the mutation spectrums of TMC1 and MYO15A and illustrated that genotype-phenotype correlation in combination with next-generation sequencing may improve the accuracy for genetic diagnosis of deafness. (hindawi.com)
• Cancer is a complex genetic disease caused by abnormal alteration (mutations) in DNA sequences that leads to dyregulation of normal cellular processes thereby driving tumor growth. (intechopen.com)

Detection9

• Here we analyze sequencing data from 151 primary UM samples using a customized bioinformatic pipeline, to improve detection of BAP1 mutations and infer the clonal relationships among genomic aberrations. (nature.com)
• Strikingly, we find BAP1 mutations and other canonical genomic aberrations usually arise in an early punctuated burst, followed by neutral evolution extending to the time of clinical detection. (nature.com)
• Here we analyze next generation sequencing (NGS) data from 151 primary UMs using a wide range of bioinformatic tools and techniques to optimize our detection of BAP1 and other mutations and CNAs, to explore their clonal relationships. (nature.com)
• Applications may be for detection of known mutations, minimal residual disease monitoring (e.g. (ukas.com)
• As the technology improves, the combined detection of SNP and larger abnormalities is becoming easier, providing an all-in-one solution for detecting multiple types of mutations. (aacc.org)
• The work 'Restriction digest screening facilitates efficient detection of site-directed mutations by CRISPR in Candida albicans' by Evans and colleagues describes a useful mutagenesis and screening strategy for the important fungal pathogen Candida albicans. (peerj.com)
• Mutations in other regions of the genome may also be informative for known VOI/VOC detection. (who.int)
• A number of tools are available for the detection of mutations that are characteristic of viruses defined as VOI/VOCs. (who.int)
• Within SCAN‐B (ClinicalTrials.gov: NCT02306096), a prospective study elucidating the transcriptomic profiles for thousands of breast cancers, we developed a RNA‐seq pipeline for detection of SNVs/indels and profiled a real‐world cohort of 3,217 breast tumors. (lu.se)

Humans2

• Indels are likely to represent between 16% and 25% of all sequence polymorphisms in humans. (wikipedia.org)
• In fact, in most known genomes, including humans, indel frequency tends to be markedly lower than that of single nucleotide polymorphisms (SNP), except near highly repetitive regions, including homopolymers and microsatellites. (wikipedia.org)

Genome7

• Indel (insertion-deletion) is a molecular biology term for an insertion or deletion of bases in the genome of an organism. (wikipedia.org)
• In coding regions of the genome, unless the length of an indel is a multiple of 3, it will produce a frameshift mutation. (wikipedia.org)
• The term "indel" has been co-opted in recent years by genome scientists for use in the sense described above. (wikipedia.org)
• The frequency of mutation and deletion of specific areas of the mitochondrial genome in tumour and matched normal tissue of patients with HBV infection was investigated in the current study. (nature.com)
• Our knowledge on the nature and rate of genome mutation in a developing organism is rudimentary. (sanger.ac.uk)
• The VOC differ from the original Wuhan virus as they have mutations across the genome. (who.int)
• Overall, these assays and approaches detect specific mutations or features such as insertions, deletions and point mutations in the SARS CoV-2 genome that are characteristic of a particular VOC/VOI using PCR. (who.int)

Tumors6

• Inactivating mutations in the tumor suppressor BAP1 are associated with the class 2 GEP and high metastatic risk 9 , whereas single nucleotide substitutions in SF3B1 and EIF1AX are found mainly in class 1 tumors and are associated with intermediate and low metastatic risk, respectively 10 , 11 . (nature.com)
• 6p Gain (6p+) is often found in class 1 tumors harboring SF3B1 and EIF1AX mutations, whereas 8q gain (8q+) can be found in both class 1 and class 2 tumors, and is associated with BAP1 and SF3B1 mutations. (nature.com)
• Multiple endocrine neoplasia syndrome type 1 (MEN-1), loss-of-function germline mutations in the tumor suppressor gene MEN1 increase the risk of developing pituitary, parathyroid and pancreatic islet tumors, and less commonly thymic carcinoids, lipomas and benign adrenocortical tumors. (intechopen.com)
• In the case of multiple endocrine neoplasia type 2 (MEN 2), gain-of-function germline mutations clustered in specific codons of the RET proto-oncogene increase the risk of developing medullary thyroid carcinoma (MTC), phaeochromocytoma and parathyroid tumors. (intechopen.com)
• Better overall survival and progression-free survival were observed in high PD-L1 expression tumors, regardless of KRAS mutation type. (bvsalud.org)
• The heterogeneous nature of KRAS-mutant tumors and the presence of other co-mutations may contribute to different outcomes to immunotherapy-based strategies. (bvsalud.org)

Genomic3

• It has been shown that genomic regions with multiple indels can also be used for species-identification procedures. (wikipedia.org)
• An obstacle to performing reliable genomic clonality analysis in UM has been an inability to detect the wide diversity of BAP1 mutations using standard bioinformatic methods. (nature.com)
• This approach reveals many previously undetected BAP1 and spliceosome mutations, and uncovers strong evidence that the canonical genomic aberrations in UM usually arise in an early, punctuated burst followed by clonal stasis. (nature.com)

Single Nucleotide1

• According to evolutionists the substitutions are almost always a single nucleotide (called a point mutation). (uncommondescent.com)

Missense mutations1

• T). Of the five mutations, three were truncated mutations, and the other two were missense mutations. (molvis.org)

CNVs1

• Study both CNVs and mutations for your constitutional studies using one assay. (agilent.com)

Deletions1

• Compared with the initially reported virulent US PEDV strains, 7 (9.7%) strains from 4 states contained insertions and deletions in the spike gene (S INDELs). (cdc.gov)

Pathogenic mutations1

• Putative pathogenic mutations of the COL11A1 gene were absent in this cohort of patients. (molvis.org)

Nucleotide1

• sgRNAs with +67 or +85 nucleotide (nt) tracrRNA tails mediated DNA cleavage at all target sites tested, with up to fivefold higher levels of indels than the corresponding crRNA-tracrRNA duplexes ( Fig. 1b and Supplementary Fig. 1a ). (cdc.gov)

TP531

• Mutations in KRAS, TP53, SMAD4, and others were similar in primary and metastatic tumor pairs. (genomeweb.com)

Genetics1

• Herein we selected a Mendelian genetics form of familial cancer such as hereditary tumor syndromic endocrine neoplasias caused by highly penetrant germline mutations leading to pheochromocytoma-paraganglioma syndromes. (intechopen.com)

Novo mutations1

• If a laboratory regularly designs primers to detect de novo mutations or for minimal residual disease monitoring, a flexible scope may be a suitable option. (ukas.com)

20171

• 2017 (which extended Neff's approach to identify CRISPR indels with their indCAPS tool). (peerj.com)

Homozygous1

• Results We identified a homozygous deleterious indel mutation in ACBD5 , leading to complete loss of ACBD5 protein in the patient. (bmj.com)

Phylogenetic1

• Sequencing complete chloroplast genomes can resolve phylogenetic relationships at low taxonomic levels and identify point mutations and indels that can be used in species identification. (usda.gov)

Deleterious1

• citation needed] Using passenger-immunoglobulin mouse models, a study found that the most prevalent indel events are the activation-induced cytidine deaminase (AID)-dependent ±1-base pair (bp) indels, which can lead to deleterious outcomes, whereas longer in-frame indels were rare outcomes. (wikipedia.org)

CRISPR2

• CRISPR/Cas9-mediated NHEJ in mouse embryos will be used to generate founder animals harboring insertion/deletion (indel) or interval deletion knockout alleles. (bcm.edu)
• High-efficiency non-mosaic CRISPR-mediated knock-in and indel mutation in F0 Xenopus. (xenbase.org)

Tumor3

• UM is also notable for having two sets of driver mutations, with each tumor typically containing one mutation from each group 2 . (nature.com)
• Approximately 20% of lung adenocarcinomas harbor activating mutations at KRAS, an oncogene with the ability to alter the tumor immune microenvironment. (bvsalud.org)
• These results add another dimension to the use of RNA‐seq as a clinical tool, where both gene expression‐ and mutation‐based biomarkers can be interrogated in real‐time within 1 week of tumor sampling. (lu.se)

Genomes1

• Launched in 2013, the 100 000 genomes project didn't just look at DNA containing harmful mutations, it also created healthy reference genomes. (aacc.org)

Pathways1

• Patients harboring mutations in actionable pathways were more likely to succumb from recurrent disease compared with those who did not, suggesting that the former should be considered for treatment with targeted compounds in future trials. (biomedcentral.com)

Syndromes1

• The following findings may be noted in these syndromes, which may overlap depending on the underlying mutation. (medscape.com)

Mutagenesis3

• Here the authors report a protein-engineering framework based on InDel mutagenesis and fragment transplantation resulting in greater catalysis and longer glow-type bioluminescence of the ancestral luciferase. (muni.cz)
• Insertion-deletion (InDel) backbone mutagenesis of Anc(HLD-RLuc) challenged the scaffold dynamics. (muni.cz)
• Small Indels in the Androgen Receptor Gene: Phenotype Implications and Mechanisms of Mutagenesis. (medscape.com)

KRAS2

• In this retrospective study, we examined 103 patients with KRAS-mutant lung adenocarcinoma who were treated with immunotherapy-based regimens and we evaluated the clinical outcomes according to PD-L1 expression and the type of KRAS mutation. (bvsalud.org)
• Among all patients included, 47% carried KRAS G12C mutation whereas 53% harbored KRAS non-G12C mutations. (bvsalud.org)

Exon3

• It is one of the most common causes of ADNSHL in Mideast countries due to prevalent consanguineous marriage [ 22 , 23 ], with majority associated with prelingual severe-to-profound hearing loss and mutations in exon 2 leading to a milder auditory phenotype [ 23 ]. (hindawi.com)
• Accession C0001 Systematic name Allele 1: g.1067C>T, c.67C>T, p.Q19X Original code III-9 (Rhode Island) Description Allele 1: point mutation in the exon 1 leading to a Description premature stop codon Description Allele 2: Not identified Date 29-May-2002 (Rel. (lu.se)
• Accession C0007 Systematic name Allele 1 and 2: g.25679C>T, c.892C>T, r.892c>u, p.Gln298X Original code BP.1 Description Allele 1 and 2: A point mutation in the exon 9 leading to a Description premature stop codon Date 03-Aug-2010 (Rel. (lu.se)

Spectrum2

• Our results expand the spectrum of known FOXL2 mutations and provide additional insight into the structure-function relationships of the FOXL2 protein. (ijbs.com)
• This is the first study in a cohort of Chinese patients with Stickler syndrome, and the results expand the mutation spectrum of the COL2A1 gene. (molvis.org)

Patients5

• Based on the patients' clinical manifestations and analysis of the identified indel mutation, we found that the mutation disturbed interactions between FOXL2 and the StAR gene. (ijbs.com)
• The percentage of control subjects harbouring D-loop mutations was 11%, which was significantly lower than that observed in both the noncancerous (49%, P =0.033) and tumour tissue (59%, P =0.014) of patients with HCC. (nature.com)
• Patients with MHA have a mutation of the MYH9 gene present in chromosomal region 22q12-13. (medscape.com)
• Analysis of the genotype-phenotype correlation showed that the early onset of high myopia with vitreous abnormalities may serve as a key indicator of Stickler syndrome, while the existence of mandibular protrusion in pediatric patients may be an efficient indicator for the absence of mutations in COL2A1 and COL11A1 . (molvis.org)
• But early results from this NGS initiative have already identified causative mutations in patients with previously undiagnosed conditions, enabling more targeted treatments and often ending years of uncertainty. (aacc.org)

Point4

• Indels can be contrasted with a point mutation. (wikipedia.org)
• An indel inserts or deletes nucleotides from a sequence, while a point mutation is a form of substitution that replaces one of the nucleotides without changing the overall number in the DNA. (wikipedia.org)
• For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. (lu.se)
• Directed evolution commonly relies on point mutations but InDels frequently occur in evolution. (muni.cz)

Occur1

• UMs are also associated with a small set of recurrent chromosome copy number alterations (CNAs), which tend to occur in the context of a specific GEP class and BSE mutation 12 . (nature.com)

Potentially1

• Experiments together with molecular modeling using NMR chemical shifts suggest that new interactions involving intrinsically disordered proteins may evolve via a low-affinity complex which is optimized by modulating direct interactions as well as dynamics, while tolerating several potentially disruptive mutations. (elifesciences.org)

Significantly1

• In addition, this indel mutation significantly increased StAR mRNA expression by disrupting the ability of the FOXL2 protein to bind to the StAR promoter and act as a repressor of this gene. (ijbs.com)

Variant2

• Each variant will have characteristic mutations or a group of mutations that is/are unique to that particular variant. (who.int)
• A deletion-insertion (delins) variant may also be known as an insertion-deletion (indel) variant. (medlineplus.gov)

Distinct1

• Screening for both activities reveals InDel mutations localized in three distinct regions that lead to altered protein dynamics (based on crystallographic B-factors, hydrogen exchange, and molecular dynamics simulations). (muni.cz)

Protein1

• Some mutations in the S gene may lead to changes in the spike protein which result in inhibition of contact and entry of the virus into human cells, however in the case of the VOC, they contain mutations in the S gene that enhance the process of contact and entry into human cells, increasing transmissibility of the virus. (who.int)

Chromosome1

• The forkhead box L2 ( FOXL2 ) gene (OMIM#605597) was mapped to the BPES critical region on chromosome 3q23, and mutations in this gene were subsequently associated with both types of BPES. (ijbs.com)

Prognostic1

• The other group consists of near-mutually exclusive mutations in BAP1 , SF3B1 , and EIF1AX ("BSE" mutations), which are strongly prognostic of metastatic risk. (nature.com)

Alterations1

• Despite a lack of previously reported NOTCH1 mutations, integrated analysis showed enrichments of alterations affecting Notch signaling in OTSCC. (biomedcentral.com)

Frequency1

• We therefore sequenced a small portion of the hypervariable D-loop region of mitochondria from individuals with HCC in matching tumour and nontumour liver tissue to determine the frequency of mitochondrial mutations. (nature.com)

Probands1

• Gross indels were not found in COL2A1 or COL11A1 in any of the probands. (molvis.org)

Identify1

• Plant J 1998 (which used a similar approach to identify site directed mutations) and Hodgens et al. (peerj.com)

Substitution1

• This paper describes computer simulations of small populations with variations in mutation rate and other factors, and produces results that are dramatically different than Haldane's low substitution limit except in certain limited situations). (uncommondescent.com)