Analysis of Structural Variants using 3 rd generation Sequencing
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1 Analysis of Structural Variants using 3 rd generation Sequencing Michael Schatz January 12, 2016 Bioinformatics / PAG / #PAGXXIV
2 Analysis of Structural Variants using 3 rd generation Sequencing Michael Schatz January 12, 2016 Bioinformatics / PAG / #PAGXXIV
3 The Resurgence of Reference Quality Genomes Michael Schatz & Daniel Rokhsar Tuesday, January 12, 4pm 6pm Town & Country - Pacific Salon 1 4:00pm 4:20pm 4:40pm 5:00pm 5:20pm 5:40pm The Resurgence of Reference Quality Genomes Michael Schatz, CSHL + JHU High Quality, Highly Contiguous Genome Assemblies Now Richard Green, Dovetail Genomics Scalable Parallel Algorithms for de novo Assembly of Complex Genomes Aydin Buluc, Lawrence Berkeley National Laboratory Using PacBio Long Reads to Generate a High Quality Reference for the Allotetraploid Coffea arabica and its Maternal Diploid Ancestor Coffea eugeniodes Marcela Yepes, Cornell University MaSuRCA Mega-Reads Assembly Technique for Haplotype Resolved Genome Assembly of Hybrid PacBio and Illumina Data Aleksey Zimin, University of Maryland How to Compare and Cluster Every Known Genome in about an Hour Sergey Koren, NHGRI
4 Structural Variations Any mutation >50bp Profound impact on genome structure and function Genome structural variation discovery and genotyping Alkan, C, Coe, BP, Eichler, EE (2011) Nature Reviews Genetics. May;12(5): doi: /nrg2958.
5 Structural Variation Sequence Signatures
6 Structural Variation Sequence Signatures Single Molecule Sequencing No amplification artifacts More uniform coverage Essentially no GC biases Long read lengths Improved mappability More likely to span breakpoints More robust split read analysis More robust assemblies PacBio Sequel >10kbp Mean Read Lengths ~$15k / Mammalian-sized genome Basepair resolution for 50bp through 50Mbp events
7 SK#BR#3' Most'commonly'used'Her2#amplified'breast'cancer'cell'line' (Davidson'et'al,'2000)' Highly'rearranged-Mammalian-genome- 80'chromosomes'instead'of'46' Numerous'chromosome'fusions,'rearrangements,'other'SVs'
8 PacBio'Long#Read'Sequencing' mean'read'length:'9'kb ' ' ' ' ' ' '72X'overall'coverage' max'read'length:'71'kb ' ' ' '' coverage Genome#wide'coverage'averages'around'54X'' Coverage'per'chromosome'varies'greatly'as'expected'from'previous'karyotyping'results'
9 Genome'structural'analysis' Assembly)based. Alignment)based. Assembly'with' Falcon'on' DNAnexus' Alignment'with' BWA#MEM' Alignment'with' MUMmer' Copy'number' analysis' SV#calling'from' split'reads'with' Sniffles. Call'variants' between' consecu[ve' alignments'with' ABVC. Call'variants' within' alignments'with' ABVC. ~'11,000'local'variants' 50'bp'<'size'<'10'kbp' Valida[ons' 661'long#range'variants' (>10kb'distance)' SplitThreader. Detailed' analysis'of'her2' amplifica[ons'
10 Genome'structural'analysis' Assembly)based. Alignment)based. Assembly'with' Falcon'on' DNAnexus' Alignment'with' BWA#MEM' Alignment'with' MUMmer' Copy'number' analysis' SV#calling'from' split'reads'with' Sniffles. Call'variants' between' consecu[ve' alignments'with' ABVC. Call'variants' within' alignments'with' ABVC. ~'11,000'local'variants' 50'bp'<'size'<'10'kbp' Valida[ons' 661'long#range'variants' (>10kb'distance)' SplitThreader. Detailed' analysis'of'her2' amplifica[ons'
11 Assembly'using'PacBio'yields'far'beber'con[guity' PacBio'+'Falcon' Illumina'+'Allpaths#LG' Number'of'sequences:'13,532' Total'sequence'length:'2.97Gb' Mean:'266'kb' Max:'19.9'Mb' N50:.2.46.Mb.. Rela[ve'to'a'genome' size'of'3'gb' Number'of'sequences:'748,955' Total'sequence'length:'2.07'Gb' Mean:'2.8'kb' Max:'61'kb' N50:.3.3.kb.
12 ABVC:'Assembly#Based'Variant#Caller' Defined'point' Inser[on' Dele[on' reference' reference' con[g' con[g' Overlapping' alignments'suggest' tandem'repeat'' Tandem'Expansions' reference' con[g' Tandem'Contrac[ons' reference' con[g' Gap'where'sequences' do'not'align'uniquely' suggests'a'repeat' Repeat'Expansions' reference' con[g' Repeat'Contrac[ons' reference' con[g'
13
14 Assembly-based analysis highly effective for local SVs (<10kbp) ~11,000 SVs between 50bp and 10kbp in size, totaling >10Mbp of variation Essentially perfect positive predictive value Alignment artifacts confound larger events (>10kbp) WGA alignments confused by large repetitive elements near SVs SV breakpoints may be poorly spanned by a contig ~100bp on one side, 1Mbp on the other
15 Genome'structural'analysis' Assembly)based. Alignment)based. Assembly'with' Falcon'on' DNAnexus' Alignment'with' BWA#MEM' Alignment'with' MUMmer' Copy'number' analysis' SV#calling'from' split'reads'with' Sniffles. Call'variants' between' consecu[ve' alignments'with' ABVC. Call'variants' within' alignments'with' ABVC. ~'11,000'local'variants' 50'bp'<'size'<'10'kbp' Valida[ons' 661'long#range'variants' (>10kb'distance)' SplitThreader. Detailed' analysis'of'her2' amplifica[ons'
16 Long Read Structural Variation Analysis Chromosome'B' Chromosome'A' Split-read analysis greatly improved by long reads Improved chances of spanning event, including nested events However, many SVs lost due to poor alignments and poor PacBio support LUMPY fails on reads that span more than 1 breakpoint, poor localization New methods in development: NGM-LR + Sniffles NGM-LR: Improve mapping of noisy long reads Sniffles: Integrates SV evidence from split alignments, alignment fidelity (CIGAR string and MD tag)
17 Mapping'a'~500bp'dele[on' BWA-MEM NGM-LR Similar issues for insertions, inversions; or Nanopore sequencing Improved seeding, improved gap scoring: convex instead of affine
18 Long#range'structural'variants'found'by'Sniffles' Her2'oncogene' 661'long#range'variants' (>10kb'distance)'
19 Long#range'structural'variants'found'by'Sniffles'
20 Long#range'structural'variants'found'by'Sniffles' Her2' Chromosome'17' Chromosome'8'
21 SplitThreader Threading SV breakpoints to Infer the history of rearrangements in complex genomes 20 CHR 1 CHR 2 ATCGCCTA GTCCATAG 80 CHR 1 ATCG 20 CCGA 100 CHR 2 GTCC ATAG
22 Her2' Chr'17' Chr'8' 1. Healthy'chromosome'17'&'8' 2. Transloca[on'into' chromosome'8' 3. Transloca[on'within' chromosome'8' 4. Complex'variant'and' inverted'duplica[on'within' chromosome'8' 5. Transloca[on'within' chromosome'8'
23 Her2' Chr'17' Chr'8' 1. Healthy'chromosome'17'&'8' 2. Transloca[on'into' chromosome'8' 3. Transloca[on'within' chromosome'8' 4. Complex'variant'and' inverted'duplica[on'within' chromosome'8' 5. Transloca[on'within' chromosome'8' Inferring the evolution of genome structure
24 Summary & Acknowledgements ABVC + SplitThreader by Maria Nattestad Assembly-based variant analysis is efficient and accurate 10s of thousands variants present in mammalian-sized genomes SplitThreader infers the evolution to genome structure Additional context as genes are moved next to new promoters and other regulatory elements NGM-LR + Sniffles by Fritz Sedazeck Correct long read mapping is essential for SV analysis Design the mapping strategy for the error model of the data Integrate all available information for robust SV calling Currently extending to other long-range mapping technologies: Oxford Nanopore, BioNano, 10X Genomics Special thanks to Dick McCombie (CSHL), John McPherson (OICR), PacBio Funding by NSF, NIH, DOE, Sloan Foundation
25 Your new office? Thank you! The Resurgence of Reference Quality Genomes Michael Schatz & Daniel Rokhsar Tuesday January 12, 4pm 6pm Town & Country - Pacific Salon 1
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