Genomes and Genes
Summary: A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.
- Bolognini R, Gerth Kahlert C, Abegg M, Bartholdi D, Mathis N, Sturm V, et al. Characterization of two novel intronic OPA1 mutations resulting in aberrant pre-mRNA splicing. BMC Med Genet. 2017;18:22 pubmed publisher..This study shows the importance of transcript analysis to determine the consequences of unclear intronic mutations in OPA1 in proximity to the intron-exon boundaries. ..
- Elsensohn M, Leblay N, Dimassi S, Campan Fournier A, Labalme A, Roucher Boulez F, et al. Statistical method to compare massive parallel sequencing pipelines. BMC Bioinformatics. 2017;18:139 pubmed publisher..98% specificity and 76.81% sensitivity for both pipelines). The method allows thus pipeline comparison and selection. It is generalizable to all types of MPS data and all pipelines. ..
- Gansmo L, Bjørnslett M, Halle M, Salvesen H, Romundstad P, Hveem K, et al. MDM2 promoter polymorphism del1518 (rs3730485) and its impact on endometrial and ovarian cancer risk. BMC Cancer. 2017;17:97 pubmed publisher..80; 95% CI?=?0.65 - 1.00). No such association was observed for ovarian cancer risk. We found the MDM2 del1518 del variant to be associated with reduced risk of endometrial cancer among individuals carrying the MDM2 SNP309TT genotype. ..
- McCusker J. Popping Out MX Cassettes from Saccharomyces cerevisiae. Cold Spring Harb Protoc. 2017;2017:pdb.prot088120 pubmed publisher..Finally, after amplifying with the appropriately designed primers, integrated counterselectable MX cassettes can be popped out to generate seamless or "scar-free" deletion mutations, as well as indel and point mutations. ..
- Burioli E, Prearo M, Houssin M. Complete genome sequence of Ostreid herpesvirus type 1 µVar isolated during mortality events in the Pacific oyster Crassostrea gigas in France and Ireland. Virology. 2017;509:239-251 pubmed publisher..This diversity raises the question of the exact origin and evolution of OsHV-1 µVar. ..
- D Elia M, Brandão M, de Andrade Ramos B, da Silva M, Miot L, dos Santos S, et al. African ancestry is associated with facial melasma in women: a cross-sectional study. BMC Med Genet. 2017;18:17 pubmed publisher..15; 95% CI 1.13 to 33.37) were associated with melasma, independently of other known risk factors. Facial melasma was independently associated with African ancestry in a highly admixed population. ..
- Simon M, Greenaway S, White J, Fuchs H, Gailus Durner V, Wells S, et al. A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains. Genome Biol. 2013;14:R82 pubmed publisher..Moreover, the sequence variants we identify provide a set of candidate genes for the phenotypic differences observed between the two strains. ..
- Zhao H, Yang J, Xu H, Zhang J. Pseudogenization of the umami taste receptor gene Tas1r1 in the giant panda coincided with its dietary switch to bamboo. Mol Biol Evol. 2010;27:2669-73 pubmed publisher..Nonetheless, additional factors are likely involved because herbivores such as cow and horse still retain an intact Tas1r1...
- Smith C, Paguirigan A, Jeschke G, Lin K, Massi E, Tarver T, et al. Heterogeneous resistance to quizartinib in acute myeloid leukemia revealed by single-cell analysis. Blood. 2017;130:48-58 pubmed publisher..These findings establish that clinical resistance to quizartinib is highly complex and reflects the underlying clonal heterogeneity of AML. ..
- Aslan Y, Tadjuidje E, Zorn A, Cha S. High-efficiency non-mosaic CRISPR-mediated knock-in and indel mutation in F0 Xenopus. Development. 2017;144:2852-2858 pubmed publisher..4-25.7% of F0 tadpoles, with germline transmission. For both CRISPR/Cas9-mediated HDR gene editing and indel mutation, the gene-edited F0 embryos are uniformly heterozygous, consistent with a mutation in only the maternal genome...
- Mutarelli M, Marwah V, Rispoli R, Carrella D, Dharmalingam G, Oliva G, et al. A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders. BMC Genomics. 2014;15 Suppl 3:S5 pubmed publisher..This resource may become a valuable tool to help dissecting the genotype underlying the disease phenotype through an improved selection of putative patient-specific causative or phenotype-associated variations. ..
- Wang Q, Rosa B, Jasmer D, Mitreva M. Pan-Nematoda Transcriptomic Elucidation of Essential Intestinal Functions and Therapeutic Targets With Broad Potential. EBioMedicine. 2015;2:1079-89 pubmed publisher..Molecular patterns conserved among IntFam proteins demonstrated large potential as therapeutic targets to inhibit intestinal cell functions with broad applications towards treatment and control of parasitic nematodes. ..
- Miyake K, Yang C, Minakuchi Y, Ohori K, Soutome M, Hirasawa T, et al. Comparison of Genomic and Epigenomic Expression in Monozygotic Twins Discordant for Rett Syndrome. PLoS ONE. 2013;8:e66729 pubmed publisher..The level of methylation in these upstream regions was inversely correlated with the level of gene expression. Thus, differences in DNA methylation patterns likely underlie the discordance in Rett phenotypes between the twins. ..
- Guo Y, Hwang L, Li J, Eades J, Yu C, Mansfield C, et al. Genetic analysis of impaired trimethylamine metabolism using whole exome sequencing. BMC Med Genet. 2017;18:11 pubmed publisher..Thus, variants in genes other than FMO3 may cause TMAU and the genetic variants identified here serve as a starting point for future studies of impaired TMA metabolism. ..
- Glogowska E, Schneider E, Maksimova Y, Schulz V, Lezon Geyda K, Wu J, et al. Novel mechanisms of PIEZO1 dysfunction in hereditary xerocytosis. Blood. 2017;130:1845-1856 pubmed publisher..These results extend the genetic heterogeneity observed in HX and indicate that various pathophysiologic mechanisms contribute to the HX phenotype. ..
- Chen Z, Grover C, Li P, Wang Y, Nie H, Zhao Y, et al. Molecular evolution of the plastid genome during diversification of the cotton genus. Mol Phylogenet Evol. 2017;112:268-276 pubmed publisher..This research provides an overview of the molecular evolution of a single, large non-recombining molecular during the diversification of this important genus. ..
- Kim J, Lee S, Kim B, Choi I, Ryser P, Kim N. Chloroplast genomes of Lilium lancifolium, L. amabile, L. callosum, and L. philadelphicum: Molecular characterization and their use in phylogenetic analysis in the genus Lilium and other allied genera in the order Liliales. PLoS ONE. 2017;12:e0186788 pubmed publisher..Phylogenetic classifications revealed some discrepancies between trees based on the cp genomes and previous classifications based on the morphology and geographic distributions...
- Ohashi T, Lemmon C, Erickson H. Fibronectin Conformation and Assembly: Analysis of Fibronectin Deletion Mutants and Fibronectin Glomerulopathy (GFND) Mutants. Biochemistry. 2017;56:4584-4591 pubmed publisher..The mutations may destabilize their FNIII domains or generate dimers of dimers by disulfide cross-linking. ..
- Say Y. The association of insertions/deletions (INDELs) and variable number tandem repeats (VNTRs) with obesity and its related traits and complications. J Physiol Anthropol. 2017;36:25 pubmed publisher..In conclusion, INDELs and VNTRs could have important functional consequences in the pathophysiology of obesity, and research on them should be continued to facilitate obesity prediction, prevention, and treatment. ..
- Maharjan R, Ferenci T. A shifting mutational landscape in 6 nutritional states: Stress-induced mutagenesis as a series of distinct stress input-mutation output relationships. PLoS Biol. 2017;15:e2001477 pubmed publisher..Altogether, our conclusion is that environments influence genetic variation as well as selection. ..
- Callari M, Sammut S, de Mattos Arruda L, Bruna A, Rueda O, Chin S, et al. Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers. Genome Med. 2017;9:35 pubmed publisher..The ITC approach increased the sensitivity up to 17.1%, without increasing the false positive rate per megabase (FPR/Mb) and its validity was confirmed in a set of clinical samples. ..
- de la Puente M, Phillips C, Fondevila M, Gelabert Besada M, Carracedo Ã, Lareu M. A forensic multiplex of nine novel pentameric-repeat STRs. Forensic Sci Int Genet. 2017;29:154-164 pubmed publisher..In the profiles from the 11-plex assay we observed an average 2.15% stutter ratio in all the pentameric loci compared to 7.32% across equivalently-sized tetrameric STRs in the Promega PowerplexÂ® ESX-17 kit. ..
- Leung M, Wang Y, Waters J, Navin N. SNES: single nucleus exome sequencing. Genome Biol. 2015;16:55 pubmed publisher..We validated our method in a fibroblast cell line, and show low allelic dropout and false-positive error rates, resulting in high detection efficiencies for single nucleotide variants (92%) and indels (85%) in single cells. ..
- Baghai T, Varallo Bedarida G, Born C, Häfner S, Schule C, Eser D, et al. A polymorphism in the angiotensin-converting enzyme gene is associated with smoking behavior. J Clin Psychiatry. 2008;69:1983-5 pubmed
- Bakker T, Giger T, Frommen J, Largiader C. Rapid molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus L., based on large Y-chromosomal insertions. J Appl Genet. 2017;58:401-407 pubmed publisher..The tests with the separate insertions gave similar results. Thus, the new molecular sexing method gave rapid and reliable results for sexing three-spined sticklebacks and is an improvement and/or alternative to existing methods. ..
- Frenkel F, Korotkova M, Korotkov E. Database of Periodic DNA Regions in Major Genomes. Biomed Res Int. 2017;2017:7949287 pubmed publisher..Totally over 60,000 periodicity sequences were found in 15 genomes including some chromosomes of the H. sapiens (partial), C. elegans, D. melanogaster, and A. thaliana genomes. ..
- Jee J, Rasouly A, Shamovsky I, Akivis Y, Steinman S, Mishra B, et al. Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing. Nature. 2016;534:693-6 pubmed
- Freidlin P, Nissan I, Luria A, Goldblatt D, Schaffer L, Kaidar Shwartz H, et al. Structure and variation of CRISPR and CRISPR-flanking regions in deleted-direct repeat region Mycobacterium tuberculosis complex strains. BMC Genomics. 2017;18:168 pubmed publisher..coli shows increased sensitivity to DNA damage and impaired chromosomal segregation, we discussed the possibility of a similar phenotype in the deleted-DR strains and Beijing family strains as both lack the cas1 gene. ..
- Heo S, Koh Y, Kim J, Jung J, Kim H, Yoon S, et al. Identification of somatic mutations using whole-exome sequencing in Korean patients with acute myeloid leukemia. BMC Med Genet. 2017;18:23 pubmed publisher..Following validation, future studies to evaluate the usefulness of these genes in genetic testing for the early diagnosis and prognostic prediction of AML patients would be worthwhile. ..
- Seo H, Park Y, Min B, Seo M, Kim J. Evaluation of exome variants using the Ion Proton Platform to sequence error-prone regions. PLoS ONE. 2017;12:e0181304 pubmed publisher..A refined calling algorithm with better polymerase may improve the performance of the Ion Proton sequencing platform. ..
- Kim B, Park J, Jo H, Koo S, Park M. Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data. PLoS ONE. 2017;12:e0182272 pubmed publisher..Herein we could suggest the accessible algorithms that selectively reduce error rates and thereby facilitate INDEL detection. Our study may also serve as a basis for understanding the accuracy and completeness of INDEL detection. ..
- Abdel Hamed A, Ghattas M, Mesbah N, Saleh S, Abo Elmatty D. Association of interleukin-1A insertion/deletion gene polymorphism and possible high risk factors with non-alcoholic fatty liver disease in Egyptian patients. Arch Physiol Biochem. 2017;123:330-333 pubmed publisher..Major D allele of IL-1A (I/D) gene polymorphism is associated with NAFLD in the Egyptian population. ..
- Xiao Q, Zhang Z, Sun H, Yang H, Xue M, Liu X, et al. Genetic variation and genetic structure of five Chinese indigenous pig populations in Jiangsu Province revealed by sequencing data. Anim Genet. 2017;48:596-599 pubmed publisher..In conclusion, the results of our study provide the first genomic overview of the genetic variants and population structures of five Chinese indigenous pig populations. ..
- Chiang C, Scott A, Davis J, Tsang E, Li X, Kim Y, et al. The impact of structural variation on human gene expression. Nat Genet. 2017;49:692-699 pubmed publisher..These results suggest that comprehensive WGS-based SV analyses will increase the power of common- and rare-variant association studies. ..
- Laurent B, Moinard M, Spataro C, Ponts N, Barreau C, Foulongne Oriol M. Landscape of genomic diversity and host adaptation in Fusarium graminearum. BMC Genomics. 2017;18:203 pubmed publisher..The annotated genetic variants discovered for this major pathogen are valuable resources for further genetic and genomic studies. ..
- Tyner J. Kinase Inhibitor Screening in Myeloid Malignancies. Hematol Oncol Clin North Am. 2017;31:693-704 pubmed publisher..By combining functional screening with genomic data, it is also possible to accelerate understanding of these mechanistic underpinnings. ..
- Diroma M, Calabrese C, Simone D, Santorsola M, Calabrese F, Gasparre G, et al. Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data. BMC Genomics. 2014;15 Suppl 3:S2 pubmed publisher..To the best of our knowledge, this is likely the most extended population-scale mitochondrial genotyping in humans enriched with the estimation of heteroplasmies. ..
- Lalonde S, Stone O, Lessard S, Lavertu A, Desjardins J, Beaudoin M, et al. Frameshift indels introduced by genome editing can lead to in-frame exon skipping. PLoS ONE. 2017;12:e0178700 pubmed publisher..Moreover, they may contribute to a better annotation of loss-of-function mutations in the human genome. ..
- Maddhuri S, Bandaru S, Bhukya C, Cingeetham V, Malempati A, Deepika M, et al. Association of CnB 5I/5D promoter gene polymorphism and serum calcineurin levels in early onset of coronary artery disease of south Indian cohort. Gene. 2017;632:1-6 pubmed publisher..19 (95% CI 1.40-7.24) and p=0.001]. The results suggest that 5-base pair deletion results in increased serum calcineurin levels and may trigger up regulation of calcineurin which mediates vascular inflammation and atherosclerosis in CAD. ..
- Chen J, Yang X, Huang X, Duan S, Long C, Chen J, et al. Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation. BMC Genomics. 2017;18:211 pubmed publisher..It may undergo cold acclimation when air temperatures are below 10 °C. Candidate genes for cold acclimation may be predominantly involved in transmembrane transporter activities. ..
- Dockter R, Elzinga D, Geary B, Maughan P, Johnson L, Tumbleson D, et al. Developing molecular tools and insights into the Penstemon genome using genomic reduction and next-generation sequencing. BMC Genet. 2013;14:66 pubmed publisher..Our objectives were to identify and validate interspecific molecular markers from four diverse Penstemon species in order to gain specific insights into the Penstemon genome...
- Kim E, Lee H, Kwon S, Lee E, Yang W, Shin K. Sequence-based diversity of 23 autosomal STR loci in Koreans investigated using an in-house massively parallel sequencing panel. Forensic Sci Int Genet. 2017;30:134-140 pubmed publisher..Consequently, an MPS analysis of an expanded set of STRs, as demonstrated in the population statistics of a Korean population, will be of great practical use in forensic genetics. ..
- Highfill C, Tran J, Nguyen S, Moldenhauer T, Wang X, Macdonald S. Naturally Segregating Variation at Ugt86Dd Contributes to Nicotine Resistance in Drosophila melanogaster. Genetics. 2017;207:311-325 pubmed publisher..Nonetheless, this putatively causative coding InDel can be a launchpad for future mechanistic exploration of xenobiotic detoxification. ..
- Fu L, Li X, Zhang W, Wang C, Wu J, Yang H, et al. A comprehensive profiling of T- and B-lymphocyte receptor repertoires from a Chinese-origin rhesus macaque by high-throughput sequencing. PLoS ONE. 2017;12:e0182733 pubmed publisher..We believe that a comprehensive profiling of immune repertoire of rhesus macaque will facilitate the human immune-related diseases studies. ..
- Drost J, van Boxtel R, Blokzijl F, Mizutani T, Sasaki N, Sasselli V, et al. Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer. Science. 2017;358:234-238 pubmed publisher..We show that signature 30 can arise from germline NTHL1 mutations. ..
- Willing E, Zaccaria S, Braga M, Stoye J. On the inversion-indel distance. BMC Bioinformatics. 2013;14 Suppl 15:S3 pubmed publisher..We also give a lower and an upper bound for the inversion-indel distance in the presence of bad components. ..