Genetic problems of DNA portraiting as part of DNA phenotyping. Review DOI
А. В. Чемерис, A.A. Khalikov, Р.Р. Гарафутдинов

и другие.

Russian Journal of Forensic Medicine, Год журнала: 2024, Номер unknown

Опубликована: Сен. 12, 2024

Forensic DNA databases are a huge help in the investigation of crimes, making it possible to identify person who left them using biological traces, provided that information about him form an STR profile is already available. The same true for unidentified corpses. When such not database, phenotyping can come rescue, allowing you restore appearance from his DNA, which used forensic practice. greatest progress has been made establishing hair color, eye skin pigmentation and some other characteristics. But main interest person’s face, situation with this yet best, although there progress. problem multiple genes responsible facial features, including pleitropic effect. advent method as GWAS (Genome-Wide Association Study) analyze many gene loci at once presence single-nucleotide substitutions associated certain involved formation human face. However, sequencing two genomes (or exomes) each inherited father mother phased haplotyped assembly their sequences become much more informative. And approach, necessary correctly select objects large number doubles closest relatives, since, without being potentially carry nucleotide substitutions, largely determine external similarity. Another cohort should be families children very similar parents, case conduct triosequencing diploid (exomes). genetic obtained way, processed machine learning artificial intelligence, make “find” desired genes, increasing reliability portraits.

Язык: Английский

Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness DOI

Ling-Yun Luo,

Hui Wu, Liming Zhao

и другие.

Nature Genetics, Год журнала: 2025, Номер unknown

Опубликована: Янв. 8, 2025

Язык: Английский

Процитировано

2
T2T-YAO: A Telomere-to-Telomere Assembled Diploid Reference Genome for Han Chinese DOI Creative Commons
Yukun He, Yanan Chu, Shuming Guo

и другие.

Genomics Proteomics & Bioinformatics, Год журнала: 2023, Номер 21(6), С. 1085 - 1100

Опубликована: Авг. 16, 2023

Since its initial release in 2001, the human reference genome has undergone continuous improvement quality, and recently released telomere-to-telomere (T2T) version - T2T-CHM13 reaches highest level of continuity accuracy after 20 years effort by working on a simplified, nearly homozygous hydatidiform mole cell line. Here, to provide an authentic complete diploid for Han Chinese, largest population world, we assembled male Chinese individual, T2T-YAO, which includes T2T assemblies all 22 + X M Y chromosomes both haploids. The quality T2T-YAO is much better than those currently available assemblies, haploid version, T2T-YAO-hp, generated selecting assembly each autosome, top fewer one error per 29.5 Mb, even higher that T2T-CHM13. Derived from individual living aboriginal region population, shows clear ancestry potential genetic ancient ancestors. Each haplotype possesses ∼ 330-Mb exclusive sequences, 3100 unique genes, tens thousands nucleotide structural variations as compared with CHM13, highlighting necessity population-stratified genome. construction accurate representative would enable precise delineation genomic advance our understandings hereditability diseases phenotypes, especially within context population.

Язык: Английский

Процитировано

25
Telomere-to-telomere phased genome assembly using error-corrected Simplex nanopore reads DOI Creative Commons
Dominik Stanojević, Dehui Lin, Sergey Nurk

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 21, 2024

Telomere-to-telomere phased assemblies have become the norm in genomics. To achieve these for diploid and even polyploid genomes, contemporary approach involves a combination of two long-read sequencing technologies: high-accuracy long reads, e.g. Pacific Biosciences (PacBio) HiFi or Oxford Nanopore (ONT) 'Duplex' ultra-long ONT 'Simplex' reads. Using different technologies increases cost required amount genomic DNA. Here, we show that comparable results are possible using error correction Simplex reads then assembling them state-of-the-art de novo assembly methods. this, developed deep learning-based HERRO framework, which corrects while carefully preserving differences related sequences. Taking into account informative positions differentiate haplotypes repeat copies, achieves an increase read accuracy up to 100-fold human genomes. By combining with Verkko assembler, high contiguity on several genomes by reconstructing many chromosomes telomere-to-telomere, including X Y. supports both R9.4.1 R10.4.1 generalizes well other species. These provide opportunity reduce genome use corrected analyze more complex levels ploidy aneuploidy.

Язык: Английский

Процитировано

15
Comprehensive discovery and functional characterization of the noncanonical proteome DOI Creative Commons
Chengyu Shi, Fangzhou Liu,

Xinwan Su

и другие.

Cell Research, Год журнала: 2025, Номер unknown

Опубликована: Янв. 10, 2025

Abstract The systematic identification and functional characterization of noncanonical translation products, such as novel peptides, will facilitate the understanding human genome provide new insights into cell biology. Here, we constructed a high-coverage peptide sequencing reference library with 11,668,944 open reading frames employed an ultrafiltration tandem mass spectrometry assay to identify peptides. Through these methods, discovered 8945 previously unannotated peptides from normal gastric tissues, cancer tissues lines, nearly half which were derived noncoding RNAs. Moreover, our CRISPR screening revealed that 1161 are involved in tumor proliferation. presence physiological function subset selected based on scores, amino acid length, various indicators, verified through Flag-knockin multiple other methods. To further characterize potential regulatory mechanisms involved, framework artificial intelligence structure prediction peptide‒protein interaction network analysis for top 100 candidates cancer-related have diverse subcellular locations participate organelle-specific processes. Further investigation interacting partners pep1-nc-OLMALINC, pep5-nc-TRHDE-AS1, pep-nc-ZNF436-AS1 pep2-nc-AC027045.3, functions mitochondrial complex assembly, energy metabolism, cholesterol respectively. We showed pep5-nc-TRHDE-AS1 pep2-nc-AC027045.3 had substantial impacts growth xenograft models. Furthermore, dysregulation four is closely correlated clinical prognosis. Taken together, study provides comprehensive proteome, highlights critical roles

Язык: Английский

Процитировано

1
Integrated analysis of the complete sequence of a macaque genome DOI
Shilong Zhang, Ning Xu,

Lianting Fu

и другие.

Nature, Год журнала: 2025, Номер unknown

Опубликована: Фев. 26, 2025

Язык: Английский

Процитировано

1
Exploring noncoding variants in genetic diseases: from detection to functional insights DOI Creative Commons

Ke Wu,

Fengxiao Bu, Yang Wu

и другие.

Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2024, Номер 51(2), С. 111 - 132

Опубликована: Янв. 4, 2024

Previous studies on genetic diseases predominantly focused protein-coding variations, overlooking the vast noncoding regions in human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled systematic identification variants. These variants can impact gene expression, regulation, chromatin conformation, thereby contributing to disease pathogenesis. Understanding mechanisms that underlie is indispensable for precisely targeted therapies implementation personalized medicine strategies. intricacies introduce a multitude challenges research opportunities. In this review, we spectrum involved diseases, along with strategies advanced their precise in-depth understanding complexity We will delve into propose potential solutions unraveling basis rare complex diseases.

Язык: Английский

Процитировано

8
Exploring gene content with pangene graphs DOI Creative Commons
Heng Li, Maximillian G. Marin, Maha Farhat

и другие.

Bioinformatics, Год журнала: 2024, Номер 40(7)

Опубликована: Июль 1, 2024

The gene content regulates the biology of an organism. It varies between species and individuals same species. Although tools have been developed to identify changes in bacterial genomes, none is applicable collections large eukaryotic genomes such as human pangenome.

Язык: Английский

Процитировано

6
Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits DOI Creative Commons
Hui Wu,

Ling-Yun Luo,

Yahui Zhang

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Ноя. 20, 2024

Abstract A complete goat ( Capra hircus ) reference genome enhances analyses of genetic variation, thus providing insights into domestication and selection in goats related species. Here, we assemble a telomere-to-telomere (T2T) gap-free (2.86 Gb) from cashmere (T2T-goat1.0), including Y chromosome 20.96 Mb. With base accuracy >99.999%, T2T-goat1.0 corrects numerous genome-wide structural errors previous assemblies adds 288.5 Mb previously unresolved regions 446 newly assembled genes to the genome. We sequence genomes five representative breeds for PacBio reads, use as identify total 63,417 variations (SVs) with up 4711 (7.42%) regions. was applied population global wild domestic goats, which revealed 32,419 SVs 25,397,794 SNPs, 870 545,026 SNPs Also, our reveal set selective variants associated (e.g., NKG2D ABCC4 traits ASIP ).

Язык: Английский

Процитировано

5
Comparative genomics of macaques and integrated insights into genetic variation and population history DOI Open Access
Shilong Zhang, Ning Xu,

Lianting Fu

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 8, 2024

ABSTRACT The crab-eating macaques ( Macaca fascicularis ) and rhesus M. mulatta are widely studied nonhuman primates in biomedical evolutionary research. Despite their significance, the current understanding of complex genomic structure differences between species requires substantial improvement. Here, we present a complete genome assembly macaque 20 haplotype-resolved assemblies to investigate regions major species. Segmental duplication is ∼42% lower, while centromeres ∼3.7 times longer than those humans. characterization ∼2 Mbp fixed genetic variants ∼240 loci highlights potential associations with metabolic two (e.g., CYP2C76 EHBP1L1 ). Additionally, hundreds alternative splicing show post-transcriptional regulation divergence these PNPO We also characterize 91 large-scale humans at single-base-pair resolution highlight impact on gene primate evolution FOLH1 PIEZO2 Finally, population genetics recapitulates speciation selective sweeps, highlighting basis reproduction tail phenotype STAB1 , SEMA3F HOXD13 In summary, integrated analysis variation greatly enhances our comprehension lineage-specific phenotypes, adaptation, evolution, thereby improving applications human diseases.

Язык: Английский

Процитировано

4
Perspectives and opportunities in forensic human, animal, and plant integrative genomics in the Pangenome era DOI
Guanglin He, Chao Liu,

Mengge Wang

и другие.

Forensic Science International, Год журнала: 2025, Номер 367, С. 112370 - 112370

Опубликована: Янв. 12, 2025

Язык: Английский

Процитировано

0