Human Desease Research based on Next Generation Sequencing. Patrick Tao Li BGI-Europe

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1 Human Desease Research based on Next Generation Sequencing Patrick Tao Li BGI-Europe S

2 genetic variants associating human disease Personal genomics with phenotype information 50% 5% 0.5% 0.05% e.g. CFTR delta 508 PCSK9 C679X e.g. MC4R ABCAl lq21.1 in SCZ Common / Rare Disease Mendelian Disorder

3 A Traceable Publication 3

4 Metagenomics Protein-DNA ChIP-Seq SEQUENCING SEQUENCIN G & SEQUENCING Trans-omics Research Protein expression Proteome Gene regulation Gene regulation whole genome/targeted region resequencing SVs, SNPs identifying, Exome sequencing whole genome sequencing targeted region sequencing DNA methylation Gene expression RNA-Seq (transcriptom) mrna, ncrna, small RNA, micro RNA, regulatory RNA Protein

Genome Analysis Target Analysis Quantitative Analysis Modification Analysis Proteomics Level

5 Total Solution for Desease Whole Genome Resequencing Exome Sequencing Target Region Sequencing DNA Level Research Gene Expression Level Transcriptome Sequencing RNA Sequencing (Quantification) Whole Genome Analysis Target Analysis Quantitative Analysis Modification Analysis Proteomics Level Expression Regulation Mechanisms Whole Genome Bisulfite Sequencing RRBS ChIP Sequencing Small RNA Sequencing

6 Disease name genes Testing list of Genetic diseases PKHD1 Autosomal Recessive Polycystic Kidney Disease, ARPKD Wilson Disease ATP7B Adenomatous Polyposis Of The Colon; APC APC Clinical practice (64) In research (89) Duchenne Type Muscular Dystrophy Marfan Syndrome Myotonia Congenita Autosomal Recessive Spastic Paraplegia 11 Mucopolysaccharidosis Type II Pendred Syndrome; PDS Neurofibromatosis Cystic Fibrosis Joubert Syndrome Maple Syrup Urine Disease Congenital Hypothyroidism diseases with high occurance DMD FBN1 CLCN1 SPG11 IDS SLC26A4 NF1,NF2 CFTR INPP5E, TMEM216, TMEM67, OFD1, NPHP1, CC2D2A, CEP290, ARL13B, AHI1, RPGRIP1L BCKDHA,BCKDHB,DBT TSHR,TSHB,NKX2-5

7 Finished genome of the deadly E. coli burst in German pty1 plasmid (89,963bp) Two antibiotics resistant genes Stx2- convey prophage Sep A pty2 plasmid (76,284bp) aggregative adherence fimbria I pty3 plasmid A composite transposon harboring multi-resistant genes

8 Geographical distribution of the 154 M. tuberculosis clinical isolates 154 clinical isolates displaying different drug resistance profiles (35 DS, 96 MDR and 23 XDR isolates) sampled from ten provinces and municipalities in China. DS: drug sensitive MDR : multi-drug-resistant XDR : extensively-drug-resistant

9 Phylogenetic tree of the 154 M. tuberculosis isolates Since lineage-specific SNPs would interfere with the detection of those associated with drug resistance, we first constructed a phylogenetic tree to: (1) check whether the tree agrees with previously reported ones (2) identify lineage-specific SNPs and remove them Phylogenetic tree of the 154 M. tuberculosis isolates in this study together with 24 previously published genomes Branch colors : pink, L1 lineage (the Philippines and the Indian Ocean Rim); blue, L2 lineage (East Asia); purple, L3 lineage (India, East Africa); red, L4 lineage (Europe, America); brown, L5, M. africanum (West Africa 1); green, L6, M. africanum (West Africa 2). Blue and red shaded regions show the sub-lineages of lineages 2 and 4, respectively. Strains labeled in grey are strains whose genomes have been published previously, those in blue are DS strains, those in black are MDR strains, and those in pink are XDR strains.

10 78 DR-associated genes and 35 intergenic regions By examining nssnps and intergenic SNPs, we found 78 genes and 35 intergenic regions associated with drug resistance. Upper figure: genomic distribution of genes/intergenic regions Outer circle: drug resistance genes; Inner circle: intergenic regions; red lines: previously reported; blue lines: discovered in this study. Lower figure: density of the drug resistance genes and intergenic regions across the genome (window, 100 Kbp; step, 500 bp). Regions of the genome where the density of DR genes is 5 genes/intergenic regions are colored dark red; those where the density is <5 genes/intergenic regions are colored light red.

11 Relative abundance of 57 frequent microbial genomes among individuals of the cohort. Bacterial species abundance differentiates IBD patients and healthy individuals. S 576.7Gb data production S S 3.3Mb non-redundant microbial genes The gene set, ~150 times larger than the human gene complement

Cervical cancer & HPV genotyping 14 high risk HPV(16 18 31 33 35 39 45 51 52 56 58 59 66 68)2 low risk (6 11)genotyping Method: 1.MALDI-TOF-MS 2.High throughput sequencing Major Work: 1.

12 Cervical cancer & HPV genotyping 14 high risk HPV( )2 low risk (6 11)genotyping Method: 1.MALDI-TOF-MS 2.High throughput sequencing Major Work: 1.Accomplished more than 60,000 women cervical cancer screening tests,demonstrating that this test is as good as classical HC2 test; 2.Donated 100,000 HPV tests for low income women in more than 10 cities 3.So far, 89,320 in total ; 7,863 postive 12

13 HBV drug resistance Detect 19 mutations associated HBV drug resistance, provide instructions for hepatitis B treatment Methods: MALDI-TOF-MS, Sequencing highly sensitive (5% mutant virus), new mutations can be discovered. Major work: More than 8000 tests 13

14 Noninvasive prenatal test-down Syndrome S Services: testing for chromosome aneuploidy diseases, maily T 21, T13, T18 S Methods: NGS S Advantages: noninvasive, safe, early stage (gestation of 12-24w), accurate, etc. 14

15 Whole Genome Profiling --Single Cell Resequencing S Cancer cell evolution during tumor progression S Large-scale epidemiological tumor research S Early diagnosis and prognosis of cancer

16 Exome / Target Region Sequencing

17 Epigenomic Research based on NGS DNA Methylation Whole Genome Bisulfite Sequencing RRBS (Reduced Representative Bisulfite Sequencing) DNA-Protein Interation ChIP Sequencing

18 DNA-Protein Interaction ChIP Sequencing S whole genome wide S Cost efficiency S Start from limited amount of ChIPed DNA: 5-10ug enrichment DNA product is available for library preparation

19 RNA Level Expression level 1, Transcriptome Sequencing 2, RNA Quantitifcation Sequencing Non-coding RNA regulation: Small RNA Sequencing

20 Proteome in BGI Proteome profiling modification proteomics Quantitative proteomics expression (different tissue/state/time) Target proteomics target protein expression Protein ID identification protein for low complexity sample 20

21 ABOUT US

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23 New-gen sequencing 137 Illumina Hi-Seq Life Tech SOLiD 4 Supercomputer: 102 T flops, 10 PB storage Applications: 1. Genome sequencing 2. RNA sequencing 3. Epigenome and ChIP-seq 4. Metagenome 23

Thank you! Patrick Tao Li litao@genomics.

24 Thank you! Patrick Tao Li Tel: ;

DNA. bioinformatics. epigenetics methylation structural variation. custom. assembly. gene. tumor-normal. mendelian. BS-seq. prediction.

DNA. bioinformatics. epigenetics methylation structural variation. custom. assembly. gene. tumor-normal. mendelian. BS-seq. prediction. Epigenomics T TM activation SNP target ncrna validation metagenomics genetics private RRBS-seq de novo trio RIP-seq exome mendelian comparative genomics DNA NGS ChIP-seq bioinformatics assembly tumor-normal