RESUMO
Human genomics is witnessing an ongoing paradigm shift from a single reference sequence to a pangenome form, but populations of Asian ancestry are underrepresented. Here we present data from the first phase of the Chinese Pangenome Consortium, including a collection of 116 high-quality and haplotype-phased de novo assemblies based on 58 core samples representing 36 minority Chinese ethnic groups. With an average 30.65× high-fidelity long-read sequence coverage, an average contiguity N50 of more than 35.63 megabases and an average total size of 3.01 gigabases, the CPC core assemblies add 189 million base pairs of euchromatic polymorphic sequences and 1,367 protein-coding gene duplications to GRCh38. We identified 15.9 million small variants and 78,072 structural variants, of which 5.9 million small variants and 34,223 structural variants were not reported in a recently released pangenome reference1. The Chinese Pangenome Consortium data demonstrate a remarkable increase in the discovery of novel and missing sequences when individuals are included from underrepresented minority ethnic groups. The missing reference sequences were enriched with archaic-derived alleles and genes that confer essential functions related to keratinization, response to ultraviolet radiation, DNA repair, immunological responses and lifespan, implying great potential for shedding new light on human evolution and recovering missing heritability in complex disease mapping.
Assuntos
População do Leste Asiático , Etnicidade , Variação Genética , Genoma Humano , Genética Humana , Grupos Minoritários , Humanos , População do Leste Asiático/classificação , População do Leste Asiático/genética , Etnicidade/genética , Genoma Humano/genética , Análise de Sequência de DNA , Raios Ultravioleta , Genética Humana/normas , Minorias Étnicas e Raciais , Padrões de Referência , Haplótipos/genética , Eucromatina/genética , Alelos , Reparo do DNA/genética , Queratinas/genética , Queratinas/metabolismo , Longevidade/genética , Imunidade/genéticaRESUMO
The human leukocyte antigen (HLA) system, or the human version of the major histocompatibility complex (MHC), is known for its extreme polymorphic nature and high heterogeneity. Taking advantage of whole-genome and whole-exome sequencing data, we developed PGG.MHC to provide a platform to explore the diversity of the MHC in Asia as well as in global populations. PGG.MHC currently archives high-resolution HLA alleles of 53 254 samples representing 190 populations spanning 66 countries. PGG.MHC provides: (i) high-quality allele frequencies for eight classical HLA loci (HLA-A, -B, -C, -DQA1, -DQB1, -DRB1, -DPA1 and -DPB1); (ii) visualization of population prevalence of HLA alleles on global, regional, and country-wide levels; (iii) haplotype structure of 134 populations; (iv) two online analysis tools including 'HLA imputation' for inferring HLA alleles from SNP genotyping data and 'HLA association' to perform case/control studies for HLA-related phenotypes and (v) East Asian-specific reference panels for HLA imputation. Equipped with high-quality frequency data and user-friendly computer tools, we expect that the PGG.MHC database can advance the understanding and facilitate applications of MHC genomic diversity in both evolutionary and medical studies. The PGG.MHC database is freely accessible via https://pog.fudan.edu.cn/pggmhc or https://www.pggmhc.org/pggmhc.
Assuntos
Bases de Dados Genéticas , Complexo Principal de Histocompatibilidade , Humanos , Alelos , Frequência do Gene , Haplótipos , Antígenos de Histocompatibilidade Classe I/genética , Antígenos de Histocompatibilidade Classe II/genética , Antígenos HLA/genética , Complexo Principal de Histocompatibilidade/genéticaRESUMO
This paper provides a new (second) way, which is completely different from Shor's algorithm, to show the optimistic potential of a D-Wave quantum computer for deciphering RSA and successfully factoring all integers within 10000. Our method significantly reduced the local field coefficient [Formula: see text] and coupling term coefficient [Formula: see text] by more than 33% and 26%, respectively, of those of Ising model, which can further improve the stability of qubit chains and improve the upper bound of integer factorization. In addition, our results obtained the best index (20-bit integer (1028171)) of quantum computing for deciphering RSA via the quantum computing software environment provided by D-Wave. Furthermore, Shor's algorithm requires approximately 40 qubits to factor the integer 1028171, which is far beyond the capacity of universal quantum computers. Thus, post quantum cryptography should further consider the potential of the D-Wave quantum computer for deciphering the RSA cryptosystem in future.