Comprehensive analysis of RNA-sequencing to find the source of every last read across 544 individuals from 53 tissues

Transcription

1 Comprehensive analysis of RNA-sequencing to find the source of every last read across 544 individuals from 53 tissues Serghei Mangul Eskin Lab (ZarLab) University of California, Los Angeles

2 RNA-Seq RNA molecules Genome A B C D E A B C A C D E (Differential) gene expressions RNA splicing Assemble novel transcripts

3 RNA-Seq reads In-silicoseparation Genotype-Tissue Expression (GTEx v6) 8,555 samples across 544 individuals from 53 body sites Human references Mapped human reads Read Origin Protocol Mangul, Serghei, et al. "Dumpster diving in RNA-sequencing to find the source of every last read." biorxiv (2016):

4 RNA-Seq 55.4M paired-end reads Read Origin Protocol Map to the human genome (tophat2) Mapped reads (87.2%) Unmapped reads (12.8%) Genomic profile of mapped reads Genomic profile of mapped reads (gprofile) Genomic profile of repeat elements (rprofile) CDS+ UTR LTR LINE SINE others introns others

5 RNA-Seq 55.4M paired-end reads Read Origin Protocol Genomic profile of unmapped reads 1. Quality control (FASTQC, SEQCLEAN) 2. Remap to human references (Megblast) low quality reads (4.8%) rrna repeat (2.0%) lost human reads (4.8%)

6 RNA-Seq 55.4M paired-end reads Read Origin Protocol Genomic profile of unmapped reads a. Quality control (FASTQC, SEQCLEAN) b. Remap to human references (Megblast) c. Map to repeat sequences (Megablast) low quality reads (4.8%) rrna repeat (2.0%) lost human reads (4.8%) lost repeat elements (0.03%)

7 Repeat profile CR1 1% ERVL-MaLR ERVL 7% 3% ERVK 1% ERV1 6% DNA 8% Retroposon 1% Satellite 0.3% Alu 33% L2 10% MIR 7% L1 23% *On average 7% (~3M) reads are categorized as repeats

8 RNA-Seq 55.4M paired-end reads Read Origin Protocol Genomic profile of unmapped reads a. Quality control (FASTQC, SEQCLEAN) b. Remap to human references (Megblast) c. Map to repeat sequences (Megablast) d. Non-co-linear (NCL) RNA profiling (ncsplice) low quality reads (4.8%) rrna repeat (2.0%) lost human reads (4.8%) lost repeat elements (0.03%) NCL RNA (0.1%) Gene A Gene B RNA Junction point Trans-splicing (gene fusion)

9 Adaptive immune repertoires Mapped reads Unmapped reads V N D N J C CDR1 CDR2 CDR3 mrna encoding for T and B cell receptor chains

10 RNA-Seq 55.4M paired-end reads Read Origin Protocol Genomic profile of unmapped reads a. Quality control (FASTQC, SEQCLEAN) b. Remap to human references (Megblast) c. Map to repeat sequences (Megablast) d. Non-co-linear (NCL) RNA profiling (ncsplice) e. B and T cell receptors profiling (ImReP) Mapped reads low quality reads (4.8%) rrna repeat (2.0%) lost human reads (4.8%) lost repeat elements (0.03%) NCL RNA (0.1%) immune reads (0.02%)

11 Spleen Small Intestine - Peyer spatch Whole Blood Artery - Coronary Artery - Tibial Minor Salivary Gland Colon - Transverse Stomach Lung Fallopian Tube Esophagus - Mucosa Liver Cervix - Ectocervix Breast - Mammary Tissue Cervix - Endocervix Vagina Kidney - Cortex Artery - Aorta Prostate Thyroid Bladder Uterus Ovary Pancreas EBV-transformed lymphocytes Transformed fibroblasts Leukemia cell line (CML) Adipose - Visceral (Omentum) Adipose - Subcutaneous Adrenal Gland Colon - Sigmoid Pituitary Nerve - Tibial Skin - Not Sun Exposed (Suprapubic) Heart - Atrial Appendage Gastroesophageal Junction Esophagus - Muscularis Skin - Sun Exposed (Lower leg) Heart - Left Ventricle Testis Brain - Cerebellar Hemisphere Brain - Frontal Cortex (BA9) Brain - Putamen (basal ganglia) Adaptive immune repertoires Number of IGH clonotypes Number of IGH derived reads per million RNA Seq reads Number of IGH derived reads per million RNA Seq reads Number of IGH clonotypes tissue Number of IGH clonotypes Cells EBV transformed lymphocytes Colon Sigmoid Lung Minor Salivary Gland Small Intestine Terminal Ileum Spleen *IGH : immunoglobulin heavy chain

12 ROP(ImRep) is able to identify samples with high activity of lymphocytes Thyroid Normal Thyroid Spleen Small Intestine Terminal Ileum Minor Salivary Gland Thyroid with chronic inflammation, atrophy Lung Colon Sigmoid Sigmoid Colon. Essentially all muscularis Sigmoid Colon. Mucosa well preserved( ~15-20% thickness)

13 Genomic profile of unmapped reads RNA-Seq a. Quality control (FASTQC, SEQCLEAN) b. Remap to human references (Megblast) c. Map to repeat sequences (Megablast) d. Non-co-linear (NCL) RNA profiling (ncsplice) e. B and T lymphocytes profiling (ImReP) f. Microbiome profiling (MCS/Megablast) 55.4M paired-end reads low quality reads (4.8%) rrna repeat (2.0%) lost human reads (4.8%) lost repeat elements (0.03%) NCL RNA (0.1%) V(D)J recombinations (0.02%) microbial reads (0.2%) unaccounted reads (0.9%) Read Origin Protocol *Mangul, Serghei, et al. "Reference-free comparison of microbial communities via de Bruijn graphs." ACM-BCB 2016 template jumping unknown microbes (EMDeBruijn*) hyper-editing (E. Levanon)

14 Human microbiome a. a. Superkindom Epstein-Barr Virus (EBV) Bacteria b. Proteobacteria Actinobacteria b. Phyla 67% 24% 8% c. Firmicutes Betaproteobacteria Gammaproteobacteria Actinobacteria Bacilli c. Class 53% d. Order 53% 16% 11% 5% 24% 13% 11% d. Burkholderiales Pseudomonadales Enterobacteriales Actinomycetales Bifidobacteriales Positive Control : Cells - EBV-transformed lymphocytes samples Lactobacillales Obtained by MetaPhlAn2 Microbial Coverage Scanner (MCS v1.0)

15 ROP tool No installation is required. The ROP comes with no pre-requirements except Python 2.7. ROP Tutorial Read Origin Protocol Lost human reads Lost repeat elements Non-co-linear RNAs V(D)J recombination (BCR/TCR) Microbial communities Typical output of ROP RNA-Seq WGS WES Chip-Seq Single cell Seq ROP is available at

16 Acknowledgment Harry Taegyun Yang Maura Rossetti Roberto Spreafico Loes Loohuis Roel A. Ophoff Eleazar Eskin Noah Zaitlen Mark Ansel Nicolas Strauli Stephanie Christenson Ryan D. Hernandez Prescott G. Woodruff GTEx Consortium David Koslicki Kevin Wesel Will Van Der Wey Jeremy Rotman Benjamin Statz Sagiv Shifman Franziska Gruhl

17 ROP protocol can find lost human reads reads within the threshold of tophat2 reads with additional mismatches and/or short gaps Percentage of lost human reads (%) 25% 20% 15% 10% 5% 15% 7% 3% 22% 12% 9% 7% 6% 6% 6% 6% 0% edit distance

18 Microbiome diversity is significantly different across tissues 3 p<10-16 Alpha diversity Adrenal gland Heart LCL Lung Hypophysis Thyroid Negative Controls Obtained by MetaPhlAn2