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Genome-wide Association Analysis
Genome-wide association study (GWAS) aims at identifying genetic variants (genotype) that associated with specific traits (phenotype). GWAS study investigates genetic markers cross whole genome of large number of individuals and predicts genotype-phenotype associations by statistical analysis at population level. It has been widely applied in research on human diseases and functional gene mining on complex traits of animals or plants.
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Plant/Animal Whole Genome Sequencing
Whole genome re-sequencing, also known as WGS, enables the revealing of both common and rare mutations on the whole genome including Single Nucleotide Polymorphism (SNP), Insertion Deletion (InDel), Structure variation (SV), and Copy Number Variation (CNV). SVs make up a larger portion of the variation base than SNPs and have a greater impact on the genome, which has a significant effect on living organisms. Long-read resequencing allows for more precise identification of large fragments and complicated variations because long reads make it much easier to chromosomal crossing over complicated regions such as tandem repeats, GC/AT-rich regions, and hyper-variable regions.
Platform: Illumina, PacBio, Nanopore
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Evolutionary Genetics
Evolutionary genetics is a packed sequencing service designed for providing a comprehensive interpretation on evolutionary information of given materials based on genetic variations, including SNPs, InDels, SVs and CNVs. It provides all fundamental analysis required for describing evolutionary changes and genetic features of populations, such as population structure, genetic diversity, phylogeny relationships, etc. It also contains studies on gene flow, which empowers estimation of effective population size, divergence time.
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Bulked Segregant analysis
Bulked segregant analysis (BSA) is a technique employed to quickly identify phenotype associated genetic markers. Main workflow of BSA contains selecting two groups of individuals with extremely opposing phenotypes, pooling the DNA of all individuals to form two bulk of DNA, identifying differential sequences between two pools. This technique has been extensively employed in identifying genetic markers strongly associated by targeted genes in plant/animal genomes.
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Comparative Genomics
Comparative genomics literally means comparing the complete genome sequences and structures of different species. This discipline aims at revealing species evolution, gene function, gene regulatory mechanism at genome level by identifying the sequence structures and elements that conserved or differentiated across different species. Typical comparative genomics study includes analyses in gene family, evolutionary development, whole genome duplication, selective pressure, etc.
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Hi-C based Genome Assembly
Hi-C is a method designed to capture chromosome configuration by combining probing proximity-based interactions and high-throughput sequencing. The intensity of these interactions is believed to be negatively correlated with physical distance on chromosomes. Therefore, Hi-C data could guide the clustering, ordering and orienting of assembled sequences in a draft genome and anchoring those onto a certain number of chromosomes. This technology empowers a chromosome-level genome assembly in absence of population-based genetic map. Every single genome needs a Hi-C.
Platform：Illumina NovaSeq6000 / DNBSEQ
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Plant/Animal De novo Genome Sequencing
De novo sequencing refers to construction of a species’ whole genome using sequencing technologies, e.g. PacBio, Nanopore, NGS, etc., in absence of a reference genome. The remarkable improvement in read length of third generation sequencing technologies has brought new opportunities in assembling complex genomes, such as those with high heterozygosity, high ratio of repetitive regions, polyploids, etc. With read length at tens of kilobases level, these sequencing reads enable resolving of repetitive elements, regions with abnormal GC contents and other highly complex regions.
Platform： PacBio Sequel II /Nanopore PromethION P48/ Illumina NovaSeq6000
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Human Whole Exome Sequencing
Whole exome sequencing (WES) is regarded as a cost-effective sequencing strategy for identifying disease-causing mutations. Although exons only take up approximately 1.7% of entire genome, it represents the profile of total protein functions directly. In human genome, it has been reported that more than 85% of disease related mutations occur in protein coding region.
BMKGENE offers comprehensive and flexible human whole exome sequencing services with different exon capturing strategies available to meet various research goals.
Platform: Illumina NovaSeq 6000
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Specific-Locus Amplified Fragment Sequencing (SLAF-Seq)
High-throughput genotyping, especially on large-scale population, is a fundamental step in genetic association studies, which provides genetic basis for functional gene discovery, evolutionary analysis, etc. Instead of deep whole genome re-sequencing, reduced representation genome sequencing (RRGS) is introduced to minimize sequencing cost per sample, while maintain reasonable efficiency on genetic marker discovery. This is commonly achieved by extracting restriction fragment within given size range, which is named reduced representation library (RRL). Specific-locus amplified fragment sequencing (SLAF-Seq) is a self-developed strategy for SNP genotyping with or without a reference genome.
Platform: Illumina NovaSeq 6000
