bionano user group meeting pag 2020 · working and application development of various sequencing...
TRANSCRIPT
AMBYSTOMA MEXICANUM
GERMLINE EVOLUTION MODEL
QUANTITATIVE TRAIT LOCIPAEDOMORPHOSIS
CHROMOSOMAL SCAFFOLDS
MENDELIAN PIGMENT MUTANTS
REPEAT-RICH GENOMES27.3 GB
ASSEMBLY
REGENERATION
CH
RO
MO
SOM
AL
HY
BR
ID
DE
LET
ION
QU
AN
TIT
AT
IVE
TR
AIT
LO
CI
PAE
DO
MO
RP
HO
SIS
REGENERATION
REGENERATION
REGENERATION
INSE
RTI
ON
RE
PE
ATS
HOMOZYGOUS MUTANTS
CHROMOSOMAL SCAFFOLDS
DE NOVO ASSEMBLY
DE NOVO ASSEMBLY
MENDELIAN PIGMENT MUTANTS
COMPLEX
DE NOVO ASSEMBLY
94% OF
CO
NTI
G 94% OF
ANNOTATED GENE MODELSQUANTITATIVE TRAIT LOCI
INSERTION
PAEDOMORPHOSIS
HYBRID SCAFFOLDING
GERMLINE
STRUCTURAL
FU
NC
TIO
NA
L G
EN
ET
IC V
AR
IAT
ION
N50
CO
NT
IG N
50
CO
NT
IG
PO
LYP
LOID
Y
RE
PE
AT
RE
GIO
NS
POLYPLOIDY
SERPIN PROTEASE INHIBITOR
PATHOGEN DEFENSE
POLYMORPHISMS
LTR
9.6 MBP
DISEASE-RESISTANCE GENES
STRUCTURAL VARIANTMAIZE GENOMICS
DIPLOIDIZATIONBIO
LOG
Y GENOME EVOLUTION AND GENE REGULATORY NETWORKS OF MANY SPECIES
INTACT TRANSPOSABLEELEMENTS
CONTIGGENOME DOUBLING
MAIZE LINEAGE
IMPROVED ASSEMBLY
A FOUNDATIONAL MODEL FOR
A FOUNDATIONAL MODEL FOR
GENOME
TRANSPOSABLE ELEMENT
FUNCTIONAL GENETIC VARIATION
LINEAGE EXPANSIONSEVOLUTION
GENETICS ANDGENOMICS
RECOMBINATION
IMP
RO
VE
D A
SSE
MB
LY C
ON
TIG
UIT
Y
GENOME-WIDE PATTERNS OF
DE NOVO ASSEMBLY
STRUCTURALVARIATION
GENETIC VARIATION
CONTIGUITY
FRAMESHIFTING INSERTION
GENOME CONTIGUITY
FRAMESHIFTING INSERTION FRAMESHIFTING DELETION
NPSR1
ECHOLOCATIONNPSR1
LRP2
INAVA
SCROTIFERA
APOBEC3 EXPANSIONPHYLLOSTOMUS DISCOLOR
CISTUGIDAE
LAURASIATHERIAHYBRID SCAFFOLDING
IL36G INACTIVATION
ME
TH
ION
INE
SU
BST
ITU
TIO
N IN
LR
P2
ON
TOLO
GY
DE
NO
VO
ASS
EM
BLY DISCOLOR
MOLOSSUS MOLOSSUS METHIONINE
CO
NTI
GNF-KB SIGNALLING PATHWAY
NF-KB SIGNALLING PATHWAY MOLOSSUS MOLOSSUS METHIONINE
ASSEMBLY
DE
LETI
ONNF-KB SIGNALING PATHWAY
ASSEMBLY
DIS
CO
VER
Y RHINOLOPHUS GENE
ASSEMBLY
DISCOLOR
NO
VE
L
ASSEMBLY
MYSTACINIDAE MYZOPODIDAE
NO
VE
L
ASSEMBLY
FRAMESHIFTING DELETION
ONTOLOGY
CHIROPTERA
CONTIGUITY
INTER-BREED
FERTILE PROGENYBOVINE GENOME
N50GENETIC IMPLICATIONS
COMPLEX
DE NOVO ASSEMBLYHAPLOTYPES
HY
BR
ID S
CA
FF
OLD
ING
ST
RU
CT
UR
AL
DE
NO
VO
HY
BR
ID
CO
NT
IGF
ER
TIL
E P
RO
GE
NY
N50 ASSEMBLY
HOMOZYGOUS INSERTIONS
HIGH-QUALITY
DISEASE DISCOVERY
ANIMAL GENOMES
DE NOVO ASSEMBLY
IMPROVED CONTIGUITY
HETEROZYGOUS DELETIONSEVOLUTIONARY BIOLOGY
TRANSFORM FARMING SELECTIVE BREEDING
BIOLOGICAL INTEREST
HETEROZYGOUS
STRUCTURAL VARIATION
HEALTHY
INVERSION
EVOLUTIONARY BIOLOGY
SELECTIVE BREEDING
DELETION
HY
BR
ID C
ON
TIG
UIT
Y
BIOLOGICAL INTEREST IMPROVED CONTIGUITY
ECOSYSTEMS
CNV
BIONANO USER GROUP MEETING PAG 2020
1:00 PM Pick up from Town and Country
1:00 PM - 2:00 PM Registration
2:00 PM - 2:10 PM Welcome
2:10 PM - 2:30 PM Recent development updates from Bionano GenomicsMark Oldakowski, Chief Operating Officer, Bionano Genomics, Inc.
2:30 PM - 3:00 PM Benchmarking ultra-high molecular weight DNA and tissue preservation protocols for the Vertebrate Genomes Project and beyond Jennifer Balacco, Research Assistant, Vertebrate Genome Lab, The Rockefeller University
3:00 PM - 3:30 PM Finished-quality assemblies of complex genomes using Bionano dataPhilippe Rigault Founder, President & CEO, Gydle, Canada
3:30 PM - 3:45 PM Break
3:45 PM - 4:15 PM Three enzymes and more - MOMS: A chromosome-level genome scaffolding tool using Multi-channel Optical Maps Qiushi Li, PhD, Assistant Professor, The Institute of Chinese Materia Medica (ICMM), China Academy of Chinese Medicine Sciences
4:15 PM - 4:45 PM Binned Bionano cmaps improved the human trio reference assembly in the context of the Vertebrate Genomes ProjectGiulio Formenti, PhD, Postdoctoral Associate, The Rockefeller University
4:45 PM - 5:15 PM Optical maps to improve our understanding of plant genome complexityArnaud Bellec, Lab Manager, INRAE-Plant Genomic Center
5:15 PM - 5:45 PM Improving the contiguity and correctness of de novo genome assembly via Bionano optical mapsStefano Lonardi, PhD, Professor and Vice Chair, University of California, Riverside
5:45 PM – 6:00 PM Closing RemarksMaggie Rougier-Chapman, Vice President, Global Marketing, Bionano Genomics, Inc.
6:00 PM – 7:00 PM Networking ReceptionBionano Genomics HQ
7:00 PM Drop off to Town and Country
BIONANO USER GROUP MEETINGJanuary 10, 2020 | 2:00 PM – 7:00 PM
2
SPEAKER
Jennifer BalaccoResearch AssistantVertebrate Genome LabThe Rockefeller University
Benchmarking ultra-high molecular weight DNA and tissue preservation protocols for the Vertebrate Genomes Project and beyond ABSTRACT Long read technologies require high quality, ultra-high molecular weight (uHMW) DNA (>5 µg and >150Kb). The Vertebrate Genomes Project (VGP) is an international and multidisciplinary project of the Genome10K (G10K) consortium, which has selected long-range genomic sequencing technologies that require large amounts of uHMW DNA. The current gold standard tissue preservation method for uHMW DNA is flash freezing with liquid nitrogen and storing at -80°C, but this is not always feasible for field collection. We present a comparative study of preservation methods for different environmental conditions and various sample types (muscle, soft tissue, and blood) across vertebrate groups (Mammals, Birds, Fish and Amphibians). This presentation includes current preliminary findings from this study, as well as a look towards future and developing methods in uHMW DNA extractions.
BIOJennifer Balacco is a research assistant at the Vertebrate Genome Lab (VGL), The Rockefeller University. Previously, she completed her master’s degree in molecular biology from Montclair State University and participated in research investigating urban brownfield soil bioremediation. Currently at the VGL, she works on extracting uHMW DNA from a diverse range of animal sample types, as well as long-read technologies as a part of the Vertebrate Genomes Project.
2:30 PM - 3:00 PM
SPEAKER
Philippe RigaultFounder, President & CEOGydle, Canada
Finished-quality assemblies of complex genomes using Bionano data ABSTRACT Gydle provides complete genome assembly and analysis solutions using Bionano optical mapping data and NGS technologies. We developed a novel optical aligner within our hybrid assembly and visualisation toolbox to enable de novo assembly, scaffolding, and sequence finishing of complex genomes. Complete chromosome pseudomolecule assemblies will be shown for complex plant genomes, demonstrating accurately resolved repeated sequences and local finishing enabled by iterative resolution.
BIOPhilippe has 28 years of international experience in genomics and bioinformatics research throughout the academic and private sectors. After graduating in engineering from École Centrale in Paris, he started his career at Généthon/CEPH in 1991 and developed bioinformatics tools to produce the first physical map of a human chromosome (Nature 1992) followed by the first physical map the whole Human Genome(Nature Genome Directory, 1995). In 1996, he joined Incyte in Palo Alto, California as a senior scientist, then became worldwide bioinformatics director for Rhône-Poulenc-Rorer pharmaceuticals (later to become Aventis). In 2001 he became director of bioinformatics at Illumina in San Diego. Philippe moved to Québec city in 2004 as a researcher at Laval University, and in 2008 he founded Gydle, a bioinformatics company developing innovative software solutions and providing data analysis services across life sciences.
3:00 PM - 3:30 PM
3
SPEAKER
Qiushi LiAssistant ProfessorThe Institute of Chinese Materia Medica (ICMM)China Academy of Chinese Medicine Sciences
3:45 PM - 4:15 PM
Three Enzymes and More - MOMS: A Chromosome-level Genome Scaffolding Tool using Multi-channel Optical Maps ABSTRACT Sequencing platforms and analysis tools are undergoing updates rapidly. What is the stable niche of Optical Maps in genomic research? Our answer is the accurate genome assembly and sensitive structural variation detection. Here, we present a multi-channel optical map scaffolding tool (MOMS), it can take as many as enzymes as you want, which imparts limitless potency to the optical maps-based scaffolding and SV detection.
An original data structure-directed node graph (DNG) was designed for representing the association between different enzyme-labeled optical maps and linkage between adjacent genomic regions. We also employed a heuristic algorithm to mine the path traversal and resolve conflicts. In the gap-filling stage, we combined the gap-aware mapping and multiple nick-site alignments. Finally, we use MOMaligner and an SSPACE translator to scaffold the genome sequences.
For the NA12878 human genome, the results show that MOMS significantly improves the contiguity and completeness of the initial assembly to scaffold N50 ~90 Mbp, incorporating more data compared to the standard hybrid scaffolding pipeline from Bionano Solve. Most of the filled gaps (48/57, 84.2%) were validated.
We also used MOMS to finish three additional genomes with high contiguity (N50 >10 Mbp) at low expense.
BIOQiushi Li is an assistant professor at the ICMM. Her research aims to understand the genetic and genomic architecture of complex traits in those species with high medicinal value. She also serves as the academic secretary to orchestrate the working and application development of various sequencing platforms in the center.
Qiushi received her Ph.D. degree in pharmacognosy from the Peking Union Medical School in 2015 after completing the BA in natural product chemistry at the Beijing University of Chinese Medicine. From 2015 to 2018, she worked as a postdoctoral research associate in Dr. Sam Yeaman’s lab at the EEB department of the University of Calgary, where she furthered her studies on evolutionary genomics in medicinal plants and stickleback fish. Now she is a core member of the research group leading by Prof. Shilin Chen at ICMM.
4
SPEAKER
Arnaud BellecLab ManagerINRAE-Plant Genomic Center
4:45 PM - 5:15 PM
Optical maps to improve our understanding of plant genome complexity ABSTRACT Plant genomes are large and complex. To understand this complexity the optical mapping provide invaluable information. Based on case studies on apricot tree, sunflower and eucalyptus, we will present results that illustrate plant specificities with respect to Bionano technology. We will consider the different steps of the process and discuss our current challenges on the analysis of structural variations and the assembly of heterozygous genomes.
BIOGraduated with a master’s degree in plant biotechnology and genomics, Arnaud Bellec started working in 2001 at INRA on the wheat BAC libraries construction and genes cloning projects. He joined the Plant Genomics Center in Toulouse (CNRGV) in 2004 to work on the conservation and analysis of plant genomic resources. The involvement of the laboratory in the sequencing consortia (wheat, barley, sunflower, etc.) allowed him to develop expertise in the field of complex genome sequencing. Today he is a member of the collegial head of the CNRGV and manages sequencing projects of various plant species within the framework of collaborations or services.
SPEAKER
Giulio FormentiPostdoctoral Associate, The Rockefeller University
4:15 PM - 4:45 PM
Binned Bionano cmaps improved the human trio reference assembly in the context of the Vertebrate Genomes Project ABSTRACT The Vertebrate Genomes Project (VGP) is aiming to generate near error-free assemblies for all vertebrate species, including human. Over the last two years, a new approach named trio-binning was proposed and progressively employed within the VGP community and by other researchers to improve the quality of diploid assemblies. Trio-binning takes advantage of the parental information to separate the long sequencing reads generated from the two haplotypes prior to assembly, leading to two full assemblies, one for each haplotype. The concept was recently applied to bionano molecules to improve the quality of cmaps, and the overall accuracy of resulting scaffolds. This appears particularly relevant to avoid scaffolding issues in the presence of structural variants between the two haplotypes. We have evaluated this approach in the current human reference generated in the context for the VGP. Our preliminary results suggest that binned cmaps led to improved assembly continuity and more accurate contig assembly and orientation within scaffolds.
BIOGiulio Formenti works as a bioinformatician in the framework of the Vertebrate Genomes Project (VGP). He co-ordinates the VGP assembly training group, where they share the VGP assembly pipeline to scientists interested in assembling high-quality genomes. This pipeline employs several sequencing technologies including PacBio long-reads, 10X linked reads, Bionano Optical Maps, Hi-C contact maps. His current research interests encompass several topics, including how to assemble organelles out of Third-Generation Sequencing data, as well as how to improve assembly pipelines using existing tools and developing radically new approaches.
5
SPEAKER
Stefano LonardiProfessor and Vice Chair University of California, Riverside
5:15 PM - 6:00 PM
Improving the Contiguity and Correctness of de novo Genome Assembly via Bionano Optical Maps ABSTRACT De novo genome assembly is a challenging computational problem due to the high repetitive content of eukaryotic genomes and the imperfections of sequencing technologies. Several assembly tools are currently available, each of which has strengths and weaknesses in dealing with the tradeoff between maximizing contiguity and minimizing assembly errors. In order to obtain the best possible assembly, it is common practice to generate multiple assemblies from several assemblers and/or parameter settings and try to identify the highest quality assembly. Unfortunately, often there is no assembly that both maximizes contiguity and minimizes assembly errors, so one has to compromise one for the other. The concept of assembly reconciliation has been proposed as a way to obtain a higher quality consensus assembly by merging or reconciling all the available assemblies. While several reconciliation methods have been introduced in the literature, we will show that none of them can consistently generate assemblies that are better than the assemblies provided in input. Then, we will propose a novel assembly reconciliation method that can take advantage of optical maps to accurately carry out assembly reconciliation. Experimental results demonstrate that our tool can double the contiguity of the assemblies without introducing mis-joins or reducing genome completeness.
BIOStefano Lonardi is Professor and Vice Chair in the Department of Computer Science and Engineering at University of California, Riverside, CA. He received his Ph.D. from Purdue University and he holds a doctorate degree in Electrical and Information Engineering from University of Padova, Italy. His research interests include computational molecular biology, bioinformatics, design of algorithms, machine learning and data mining. He is a Fellow of the IEEE and AAAS, and an ACM Distinguished Scientist.
RSVP
Bionano Genomics Events at PAG 2020
Bionano Genomics WorkshopMonday, Jan 13, 2020 | 4:00 - 6:10pmTown and Country Hotel, Room East 2
Gene & Tonic with SaphyrSaturday, Jan 11, 2020 | 6:30 - 9:30pmHandlery Hotel, Palm Area
6
BIONANO GENOMICSSELECT PUBLICATIONS - GENOME ASSEMBLY
The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxinsNATURE GENETICS 2020Suryamohan et al.
A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colourNATURE COMMUNICATIONS 2019Zhang et al.
Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han GenomeGENOMICS PROTEOMICS BIOINFORMATICS 2019Du et al.
Construction and comparison of three reference-quality genome assemblies for soybean.THE PLANT JOURNAL 2019Valliyodan et al.
Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivarsBMC BIOLOGY 2019Kuon et al.
Improved Genome Sequence of Wild Emmer Wheat Zavitan with the Aid of Optical MapsG3: GENES, GENOMES, GENETICS 2019Zhu et al.
The Genome of C57BL/6J “Eve”, the Mother of the Laboratory Mouse Genome Reference StrainG3: GENES, GENOMES, GENETICS 2019Sarsani et al.
Reference Genome Sequences of Two CultivatedAllotetraploid Cottons, Gossypium hirsutum and Gossypium barbadenseNATURE GENETICS 2018Wang et al.
SMRT Long Reads and Direct Label and Stain Optical Maps Allow the Generation of A High-Quality Genome Assembly for the European Barn Swallow (Hirundo rustica rustica)GIGASCIENCE 2018Formenti et al.
A Chromosome-scale Assembly of the Sorghum Genome Using Nanopore Sequencing and Optical MappingNATURE COMMUNICATIONS 2018Deschamps et al.
Improved Reference Genome of Aedes aegypti Informs Arbovirus Vector ControlNATURE 2018Matthews et al.
Genome Sequence of the Progenitor of Wheat A Subgenome Triticum urartuNATURE 2018Ling et al.
High-resolution Comparative Analysis of Great Ape GenomesSCIENCE 2018Kronenberg et al.
The Axolotl Genome and the Evolution of Key Tissue Formation RegulatorsNATURE 2018Nowoshilow et al.
Improved Maize Reference Genome with Single-molecule TechnologiesNATURE 2017Jiao et al.
Single-molecule Sequencing and Chromatin Conformation Capture Enable De Novo Reference Assembly of the Domestic Goat GenomeNATURE GENETICS 2017 Bickhart et al.
CONTIGUITY
INTER-BREED
FERTILE PROGENYBOVINE GENOME
N50GENETIC IMPLICATIONS
COMPLEX
DE NOVO ASSEMBLYHAPLOTYPES
HY
BR
ID S
CA
FF
OLD
ING
ST
RU
CT
UR
AL
DE
NO
VO
HY
BR
ID
CO
NT
IGF
ER
TIL
E P
RO
GE
NY
N50 ASSEMBLY
HOMOZYGOUS INSERTIONS
HIGH-QUALITY
DISEASE DISCOVERY
ANIMAL GENOMES
DE NOVO ASSEMBLY
IMPROVED CONTIGUITY
HETEROZYGOUS DELETIONSEVOLUTIONARY BIOLOGY
TRANSFORM FARMING SELECTIVE BREEDING
BIOLOGICAL INTEREST
HETEROZYGOUS
STRUCTURAL VARIATION
HEALTHY
INVERSION
EVOLUTIONARY BIOLOGY
SELECTIVE BREEDING
DELETION
HY
BR
ID C
ON
TIG
UIT
Y
BIOLOGICAL INTEREST IMPROVED CONTIGUITY
ECOSYSTEMS
CNV
STRUCTURAL
FU
NC
TIO
NA
L G
EN
ET
IC V
AR
IAT
ION
N50
CO
NT
IG N
50
CO
NT
IG
PO
LYP
LOID
Y
RE
PE
AT
RE
GIO
NS
POLYPLOIDY
SERPIN PROTEASE INHIBITOR
PATHOGEN DEFENSE
POLYMORPHISMS
LTR
9.6 MBP
DISEASE-RESISTANCE GENES
STRUCTURAL VARIANTMAIZE GENOMICS
DIPLOIDIZATIONBIO
LOG
Y GENOME EVOLUTION AND GENE REGULATORY NETWORKS OF MANY SPECIES
INTACT TRANSPOSABLEELEMENTS
CONTIGGENOME DOUBLING
MAIZE LINEAGE
IMPROVED ASSEMBLY
A FOUNDATIONAL MODEL FOR
A FOUNDATIONAL MODEL FOR
GENOME
TRANSPOSABLE ELEMENT
FUNCTIONAL GENETIC VARIATION
LINEAGE EXPANSIONSEVOLUTION
GENETICS ANDGENOMICS
RECOMBINATION
IMP
RO
VE
D A
SSE
MB
LY C
ON
TIG
UIT
Y
GENOME-WIDE PATTERNS OF
DE NOVO ASSEMBLY
STRUCTURALVARIATION
GENETIC VARIATION
CONTIGUITY
AMBYSTOMA MEXICANUM
GERMLINE EVOLUTION MODEL
QUANTITATIVE TRAIT LOCIPAEDOMORPHOSIS
CHROMOSOMAL SCAFFOLDS
MENDELIAN PIGMENT MUTANTS
REPEAT-RICH GENOMES27.3 GB
ASSEMBLY
REGENERATION
CH
RO
MO
SOM
AL
HY
BR
ID
DE
LET
ION
QU
AN
TIT
AT
IVE
TR
AIT
LO
CI
PAE
DO
MO
RP
HO
SIS
REGENERATION
REGENERATION
REGENERATION
INSE
RTI
ON
RE
PE
ATS
HOMOZYGOUS MUTANTS
CHROMOSOMAL SCAFFOLDS
DE NOVO ASSEMBLY
DE NOVO ASSEMBLY
MENDELIAN PIGMENT MUTANTS
COMPLEX
DE NOVO ASSEMBLY
94% OF
CO
NTI
G 94% OF
ANNOTATED GENE MODELSQUANTITATIVE TRAIT LOCI
INSERTION
PAEDOMORPHOSIS
HYBRID SCAFFOLDING
GERMLINE
FRAMESHIFTING INSERTION
GENOME CONTIGUITY
FRAMESHIFTING INSERTION FRAMESHIFTING DELETION
NPSR1
ECHOLOCATIONNPSR1
LRP2
INAVA
SCROTIFERA
APOBEC3 EXPANSIONPHYLLOSTOMUS DISCOLOR
CISTUGIDAE
LAURASIATHERIAHYBRID SCAFFOLDING
IL36G INACTIVATION
ME
TH
ION
INE
SU
BST
ITU
TIO
N IN
LR
P2
ON
TOLO
GY
DE
NO
VO
ASS
EM
BLY DISCOLOR
MOLOSSUS MOLOSSUS METHIONINE
CO
NTI
GNF-KB SIGNALLING PATHWAY
NF-KB SIGNALLING PATHWAY MOLOSSUS MOLOSSUS METHIONINE
ASSEMBLY
DE
LETI
ONNF-KB SIGNALING PATHWAY
ASSEMBLY
DIS
CO
VER
Y RHINOLOPHUS GENE
ASSEMBLY
DISCOLOR
NO
VE
L
ASSEMBLY
MYSTACINIDAE MYZOPODIDAE
NO
VE
L
ASSEMBLY
FRAMESHIFTING DELETION
ONTOLOGY
CHIROPTERA
7
Please take a few minutes to
complete our survey. Scan the
QR code on the left to start.
Share your feedback on the UGM! For general information about Bionano Genomics, please contact:
858.888.7600
bionanogenomics.com
For Research Use Only. Not for use in diagnostic procedures. Bionano Genomics®, Saphyr®, Saphyr Chip®, Bionano Access® and Bionano EnFocus™ are trademarks of Bionano Genomics Inc. All other trademarks are the sole property of their respective owners.© 2020 Bionano Genomics, Inc.