يعرض 1 - 10 نتائج من 27 نتيجة بحث عن '"INDEL Mutation/*genetics"', وقت الاستعلام: 0.91s تنقيح النتائج
  1. 1
    دورية أكاديمية

    المؤلفون: Moriot, A., Hall, D.

    المصدر: Genetics in medicine, vol. 21, no. 3, pp. 613-621

    الوصف: With the description of circulating fetal DNA in maternal blood, noninvasive prenatal diagnostics became theoretically possible. As the presence of background maternal DNA interferes with the detection of fetal DNA, analytical methods require genetic markers capable of distinguishing by quantitative or targeted approaches the minor population of DNA molecules of the fetus. Here we evaluate the feasibility of analyzing fetal DNA with novel DIP-STR genetic markers, designed for the investigation of forensic mixed biological evidence. The DIP-STR molecular approach is based on sequence-specific analysis of paternally inherited fetal alleles. These sequences are biallelic deletion/insertion polymorphisms (DIPs) located very close to short tandem repeat (STR) markers, for combined analysis. In this study, 48 women were tested with 28 DIP-STRs during the first, second, and third trimester of pregnancy. Positive results were obtained across markers, including longer ones (386 base-pairs) and with blood samples collected during early pregnancy, such as 10 weeks of gestational age. These data show that DIP-STR markers can be used to amplify specific genomic regions of circulating fetal DNA to obtain targeted genetic information. This method may contribute to developments in noninvasive prenatal paternity testing and diagnosis of certain genetic diseases.

    وصف الملف: application/pdf

    العلاقة: info:eu-repo/semantics/altIdentifier/pmid/30072742; info:eu-repo/semantics/altIdentifier/eissn/1530-0366; info:eu-repo/semantics/altIdentifier/urn/urn:nbn:ch:serval-BIB_39BEF9A322ED0; https://serval.unil.ch/notice/serval:BIB_39BEF9A322EDTest; urn:issn:1098-3600; https://serval.unil.ch/resource/serval:BIB_39BEF9A322ED.P001/REF.pdfTest; http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_39BEF9A322ED0Test

  2. 2
    دورية أكاديمية

    المؤلفون: Baldassari, Sara, Picard, Fabienne, Verbeek, Nienke E, van Kempen, Marjan, Brilstra, Eva H, Lesca, Gaetan, Conti, Valerio, Guerrini, Renzo, Bisulli, Francesca, Licchetta, Laura, Pippucci, Tommaso, Tinuper, Paolo, Hirsch, Edouard, de Saint Martin, Anne, Chelly, Jamel, Rudolf, Gabrielle, Chipaux, Mathilde, Ferrand-Sorbets, Sarah, Dorfmüller, Georg, Sisodiya, Sanjay, Balestrini, Simona, Schoeler, Natasha, Hernandez-Hernandez, Laura, Krithika, S, Oegema, Renske, Hagebeuk, Eveline, Gunning, Boudewijn, Deckers, Charles, Berghuis, Bianca, Wegner, Ilse, Niks, Erik, Jansen, Floor E, Braun, Kees, de Jong, Daniëlle, Rubboli, Guido, Talvik, Inga, Sander, Valentin, Uldall, Peter, Jacquemont, Marie-Line, Nava, Caroline, Leguern, Eric, Julia, Sophie, Gambardella, Antonio, d'Orsi, Giuseppe, Crichiutti, Giovanni, Faivre, Laurence, Darmency, Veronique, Benova, Barbora, Krsek, Pavel, Biraben, Arnaud, Lebre, Anne-Sophie, Jennesson, Mélanie, Sattar, Shifteh, Marchal, Cécile, Nordli, Douglas R, Lindstrom, Kristin, Striano, Pasquale, Lomax, Lysa Boissé, Kiss, Courtney, Bartolomei, Fabrice, Lepine, Anne Fabienne, Schoonjans, An-Sofie, Stouffs, Katrien, Jansen, Anna, Panagiotakaki, Eleni, Ricard-Mousnier, Brigitte, Thevenon, Julien, de Bellescize, Julitta, Catenoix, Hélène, Dorn, Thomas, Zenker, Martin, Müller-Schlüter, Karen, Brandt, Christian, Krey, Ilona, Polster, Tilman, Wolff, Markus, Balci, Meral, Rostasy, Kevin, Achaz, Guillaume, Zacher, Pia, Becher, Thomas, Cloppenborg, Thomas, Yuskaitis, Christopher J, Weckhuysen, Sarah, Poduri, Annapurna, Lemke, Johannes R, Møller, Rikke S, Baulac, Stéphanie

    المصدر: Baldassari , S , Picard , F , Verbeek , N E , van Kempen , M , Brilstra , E H , Lesca , G , Conti , V , Guerrini , R , Bisulli , F , Licchetta , L , Pippucci , T , Tinuper , P , Hirsch , E , de Saint Martin , A , Chelly , J , Rudolf , G , Chipaux , M , Ferrand-Sorbets , S , Dorfmüller , G , Sisodiya , S , Balestrini , S , Schoeler , N , Hernandez-Hernandez , L , Krithika , ....

    الوصف: PURPOSE: To define the phenotypic and mutational spectrum of epilepsies related to DEPDC5, NPRL2 and NPRL3 genes encoding the GATOR1 complex, a negative regulator of the mTORC1 pathway METHODS: We analyzed clinical and genetic data of 73 novel probands (familial and sporadic) with epilepsy-related variants in GATOR1-encoding genes and proposed new guidelines for clinical interpretation of GATOR1 variants. RESULTS: The GATOR1 seizure phenotype consisted mostly in focal seizures (e.g., hypermotor or frontal lobe seizures in 50%), with a mean age at onset of 4.4 years, often sleep-related and drug-resistant (54%), and associated with focal cortical dysplasia (20%). Infantile spasms were reported in 10% of the probands. Sudden unexpected death in epilepsy (SUDEP) occurred in 10% of the families. Novel classification framework of all 140 epilepsy-related GATOR1 variants (including the variants of this study) revealed that 68% are loss-of-function pathogenic, 14% are likely pathogenic, 15% are variants of uncertain significance and 3% are likely benign. CONCLUSION: Our data emphasize the increasingly important role of GATOR1 genes in the pathogenesis of focal epilepsies (>180 probands to date). The GATOR1 phenotypic spectrum ranges from sporadic early-onset epilepsies with cognitive impairment comorbidities to familial focal epilepsies, and SUDEP.

    وصف الملف: application/pdf

  3. 3

    المساهمون: Hubrecht Institute for Developmental Biology and Stem Cell Research

    المصدر: Nature Genetics, 54(10), 1564-1571. Nature Publishing Group
    NATURE GENETICS
    Nat Genet

    الوصف: Single-cell DNA sequencing data are generated from human neurons using primary template-directed amplification and analyzed using SCAN2, an improved genotyping tool. Indels are enriched in neuronal regulatory elements and may be deleterious. Accurate somatic mutation detection from single-cell DNA sequencing is challenging due to amplification-related artifacts. To reduce this artifact burden, an improved amplification technique, primary template-directed amplification (PTA), was recently introduced. We analyzed whole-genome sequencing data from 52 PTA-amplified single neurons using SCAN2, a new genotyper we developed to leverage mutation signatures and allele balance in identifying somatic single-nucleotide variants (SNVs) and small insertions and deletions (indels) in PTA data. Our analysis confirms an increase in nonclonal somatic mutation in single neurons with age, but revises the estimated rate of this accumulation to 16 SNVs per year. We also identify artifacts in other amplification methods. Most importantly, we show that somatic indels increase by at least three per year per neuron and are enriched in functional regions of the genome such as enhancers and promoters. Our data suggest that indels in gene-regulatory elements have a considerable effect on genome integrity in human neurons.

    وصف الملف: application/octet-stream

  4. 4
    دورية أكاديمية

    المصدر: Wala , J A , Bandopadhayay , P , Greenwald , N F , O'Rourke , R , Sharpe , T , Stewart , C , Schumacher , S , Li , Y , Weischenfeldt , J , Yao , X , Nusbaum , C , Campbell , P , Getz , G , Meyerson , M , Zhang , C-Z , Imielinski , M & Beroukhim , R 2018 , ' SvABA : genome-wide detection of structural variants and indels by local assembly ' , Genome Research , vol. 28 , no. 4 , pp. 581-591 . https://doi.org/10.1101/gr.221028.117Test

    الوصف: Structural variants (SVs), including small insertion and deletion variants (indels), are challenging to detect through standard alignment-based variant calling methods. Sequence assembly offers a powerful approach to identifying SVs, but is difficult to apply at scale genome-wide for SV detection due to its computational complexity and the difficulty of extracting SVs from assembly contigs. We describe SvABA, an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements. We evaluated SvABA's performance on the NA12878 human genome and in simulated and real cancer genomes. SvABA demonstrates superior sensitivity and specificity across a large spectrum of SVs and substantially improves detection performance for variants in the 20-300 bp range, compared with existing methods. SvABA also identifies complex somatic rearrangements with chains of short (<1000 bp) templated-sequence insertions copied from distant genomic regions. We applied SvABA to 344 cancer genomes from 11 cancer types and found that short templated-sequence insertions occur in ∼4% of all somatic rearrangements. Finally, we demonstrate that SvABA can identify sites of viral integration and cancer driver alterations containing medium-sized (50-300 bp) SVs.

    وصف الملف: application/pdf

  5. 5
    دورية أكاديمية
  6. 6
    دورية أكاديمية

    المصدر: G3, vol. 7, no. 8, pp. 2413-2426

    الوصف: Candida glabrata is an important fungal pathogen which develops rapid antifungal resistance in treated patients. It is known that azole treatments lead to antifungal resistance in this fungal species and that multidrug efflux transporters are involved in this process. Specific mutations in the transcriptional regulator PDR1 result in upregulation of the transporters. In addition, we showed that the PDR1 mutations can contribute to enhance virulence in animal models. In this study, we were interested to compare genomes of two specific C. glabrata -related isolates, one of which was azole susceptible (DSY562) while the other was azole resistant (DSY565). DSY565 contained a PDR1 mutation (L280F) and was isolated after a time-lapse of 50 d of azole therapy. We expected that genome comparisons between both isolates could reveal additional mutations reflecting host adaptation or even additional resistance mechanisms. The PacBio technology used here yielded 14 major contigs (sizes 0.18-1.6 Mb) and mitochondrial genomes from both DSY562 and DSY565 isolates that were highly similar to each other. Comparisons of the clinical genomes with the published CBS138 genome indicated important genome rearrangements, but not between the clinical strains. Among the unique features, several retrotransposons were identified in the genomes of the investigated clinical isolates. DSY562 and DSY565 each contained a large set of adhesin-like genes (101 and 107, respectively), which exceed by far the number of reported adhesins (63) in the CBS138 genome. Comparison between DSY562 and DSY565 yielded 17 nonsynonymous SNPs (among which the was the expected PDR1 mutation) as well as small size indels in coding regions (11) but mainly in adhesin-like genes. The genomes contained a DNA mismatch repair allele of MSH2 known to be involved in the so-called hyper-mutator phenotype of this yeast species and the number of accumulated mutations between both clinical isolates is consistent with the presence of a MSH2 defect. In conclusion, this study is ...

    وصف الملف: application/pdf

    العلاقة: info:eu-repo/semantics/altIdentifier/pmid/28663342; info:eu-repo/semantics/altIdentifier/eissn/2160-1836; info:eu-repo/semantics/altIdentifier/urn/urn:nbn:ch:serval-BIB_CDBF97BBE25A9; https://serval.unil.ch/notice/serval:BIB_CDBF97BBE25ATest; urn:issn:2160-1836; https://serval.unil.ch/resource/serval:BIB_CDBF97BBE25A.P001/REF.pdfTest; http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_CDBF97BBE25A9Test

  7. 7
    دورية أكاديمية

    المصدر: Skov , L , Schierup , M H , Danish Pan Genome Consortium , Sørensen , L M , Petersen , B , Sibbesen , J A , Liu , S , Belling , K G , Have , C T , Bork-Jensen , J , Hansen , T , Krogh , A , Sørensen , T I A , Pedersen , O B , Rasmussen , S , Kristiansen , K & Brunak , S 2017 , ' Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion ' , ....

    الوصف: The human Y-chromosome does not recombine across its male-specific part and is therefore an excellent marker of human migrations. It also plays an important role in male fertility. However, its evolution is difficult to fully understand because of repetitive sequences, inverted repeats and the potentially large role of gene conversion. Here we perform an evolutionary analysis of 62 Y-chromosomes of Danish descent sequenced using a wide range of library insert sizes and high coverage, thus allowing large regions of these chromosomes to be well assembled. These include 17 father-son pairs, which we use to validate variation calling. Using a recent method that can integrate variants based on both mapping and de novo assembly, we genotype 10898 SNVs and 2903 indels (max length of 27241 bp) in our sample and show by father-son concordance and experimental validation that the non-recurrent SNP and indel variation on the Y chromosome tree is called very accurately. This includes variation called in a 0.9 Mb centromeric heterochromatic region, which is by far the most variable in the Y chromosome. Among the variation is also longer sequence-stretches not present in the reference genome but shared with the chimpanzee Y chromosome. We analyzed 2.7 Mb of large inverted repeats (palindromes) for variation patterns among the two palindrome arms and identified 603 mutation and 416 gene conversions events. We find clear evidence for GC-biased gene conversion in the palindromes (and a balancing AT mutation bias), but irrespective of this, also a strong bias towards gene conversion towards the ancestral state, suggesting that palindromic gene conversion may alleviate Muller's ratchet. Finally, we also find a large number of large-scale gene duplications and deletions in the palindromic regions (at least 24) and find that such events can consist of complex combinations of simultaneous insertions and deletions of long stretches of the Y chromosome.

  8. 8
    دورية أكاديمية

    المصدر: Luquette , L J , Miller , M B , Zhou , Z , Bohrson , C L , Zhao , Y , Jin , H , Gulhan , D , Ganz , J , Bizzotto , S , Kirkham , S , Hochepied , T , Libert , C , Galor , A , Kim , J , Lodato , M A , Garaycoechea , J I , Gawad , C , West , J , Walsh , C A & Park , P J 2022 , ' Single-cell genome sequencing of human neurons identifies somatic point mutation ....

    الوصف: Accurate somatic mutation detection from single-cell DNA sequencing is challenging due to amplification-related artifacts. To reduce this artifact burden, an improved amplification technique, primary template-directed amplification (PTA), was recently introduced. We analyzed whole-genome sequencing data from 52 PTA-amplified single neurons using SCAN2, a new genotyper we developed to leverage mutation signatures and allele balance in identifying somatic single-nucleotide variants (SNVs) and small insertions and deletions (indels) in PTA data. Our analysis confirms an increase in nonclonal somatic mutation in single neurons with age, but revises the estimated rate of this accumulation to 16 SNVs per year. We also identify artifacts in other amplification methods. Most importantly, we show that somatic indels increase by at least three per year per neuron and are enriched in functional regions of the genome such as enhancers and promoters. Our data suggest that indels in gene-regulatory elements have a considerable effect on genome integrity in human neurons.

  9. 9
    دورية أكاديمية

    المساهمون: Eun Hye Kim, Hwan Young Lee, In Seok Yang, Woo Ick Yang, Kyoung-Jin Shin, Kim, Eun Hye, Shin, Kyoung Jin, Yang, Woo Ick, Yang, In Seok, Lee, Hwan Young

    الوصف: This study reports on the forensic parameters of 30 insertion�밺eletion polymorphisms (Indels) (Investigator DIPplex짰 kit) in 100 individuals from a Korean population. The match probability ranged from 0.353 to 0.789, and the combined power of discrimination reached 0.99999999995. The DIPplex짰 kit is more discriminative in Koreans than six COfiler짰 short tandem repeats (STRs), but less discriminative than nine Profiler Plus짰 STRs. This study further demonstrated that some Indels in the DIPplex짰 kit could be used as Asian ancestry informative markers through a comparison with other population data. ; open

    وصف الملف: 51~52

    العلاقة: INTERNATIONAL JOURNAL OF LEGAL MEDICINE; J01126; OAK-2014-00168; https://ir.ymlib.yonsei.ac.kr/handle/22282913/98088Test; http://link.springer.com/article/10.1007%2Fs00414-013-0851-6Test; T201400261; INTERNATIONAL JOURNAL OF LEGAL MEDICINE, Vol.128(1) : 51-52, 2014

  10. 10
    دورية أكاديمية