Presentation by Justin Zook at GRC/GIAB ASHG 2017 workshop "Getting the most from the reference assembly and reference materials" on benchmarks for indels and structural variants.
Presentation by Justin Zook at GRC/GIAB ASHG 2017 workshop "Getting the most from the reference assembly and reference materials" on benchmarks for indels and structural variants.
Towards Precision Medicine: Tute Genomics, a cloud-based application for anal...Reid Robison
Tute Genomics is cloud-based software that can rapidly analyze entire human genomes. The cost of whole genome sequencing is dropping rapidly and we are in the middle of a genomic revolution. Tute is opening a new door for personalized medicine by helping researchers & healthcare organizations analyze human genomes.
Moving Towards a Validated High Throughput Sequencing Solution for Human Iden...Thermo Fisher Scientific
Presented by Jennifer D. Churchill, PhD during a special Lunch and Learn session during the American Academy of Forensic Sciences (AAFS) 67th annual conference, February 2015. / Conclusions
• Robust panels of identity and ancestry SNPs
• Robust STR panel
• Whole genome mtDNA sequencing
• Highly informative
• Sensitive
• Quantitative – scaling comparison
• Low density chip is not necessarily a bad chip
• Wide range of density can still yield high quality data
• Based on results continue development and validation
Speaker: Benedict C. S. Cross, PhD, Team leader (Discovery Screening), Horizon Discovery
CRISPR–Cas9 mediated genome editing provides a highly efficient way to probe gene function. Using this technology, thousands of genes can be knocked out and their function assessed in a single experiment. We have conducted over 150 of these complex and powerful screens and will use our experience to guide you through the process of screen design, performance and analysis.
We'll be discussing:
• How to use CRISPR screening for target ID and validation, understanding drug MOA and patient stratification
• The screen design, quality control and how to evaluate success of your screening program
• Horizon’s latest developments to the platform
• Horizon’s novel approaches to target validation screening
Advances and Applications Enabled by Single Cell TechnologyQIAGEN
Over the past 5 years, single-cell genomics have become a powerful technology for studying small samples and rare cells, and for dissecting complex populations such as heterogeneous tumors. Single-cell technology is enabling many new insights into diverse research areas from oncology, immunology and microbiology to neuroscience, stem cell and developmental biology. This webinar introduces single-cell technology and summarizes the newest scientific applications in various research areas, all in the context of current literature.
Molecular QC: Interpreting your Bioinformatics PipelineCandy Smellie
What is the impact of assay failure in your laboratory and how do you monitor for it?
The most heavily degraded samples are not suitable for standard exome coverage: sometimes it’s not even a matter of getting bad sequencing, you might get nothing at all!
FFPE artifacts increase with storage time
Artifacts go against the statistical power of your variant calling analysis
Molecular reference standards help filter out bad mappings and spurious variants
Bioinformatics pipelines allow adding Molecular Reference Standards in your joint variant calling pipeline
Genome In A Bottle Reference Standards are invaluable for validating variant calling analysis
NIST and its collaborators shared datasets created with most NGS technologies
Horizon Diagnostics shared annotated, merged variant calls from NIST for the Ashkenazim Trio
~35K variants are predicted having high or moderate impact within the Trio
GM24385 (Ashkenazim Son) includes 352 small variants with high/moderate impact which are absent in Father and Mother
Routinely monitor the performance of your workflows and assays with independent external controls
In this presentation we showcase the latest advancements in myeloid genomic profiling: The Ion Torrent Oncomine Myeloid Assay GX.
Learn how this solution addresses key challenges in myeloid molecular testing and see recent data from the University of Pennsylvania.
Learn more at www.oncomine.com/myeloid
Couples presenting to the infertility clinic- Do they really have infertility...Sujoy Dasgupta
Dr Sujoy Dasgupta presented the study on "Couples presenting to the infertility clinic- Do they really have infertility? – The unexplored stories of non-consummation" in the 13th Congress of the Asia Pacific Initiative on Reproduction (ASPIRE 2024) at Manila on 24 May, 2024.
- Video recording of this lecture in English language: https://youtu.be/lK81BzxMqdo
- Video recording of this lecture in Arabic language: https://youtu.be/Ve4P0COk9OI
- Link to download the book free: https://nephrotube.blogspot.com/p/nephrotube-nephrology-books.html
- Link to NephroTube website: www.NephroTube.com
- Link to NephroTube social media accounts: https://nephrotube.blogspot.com/p/join-nephrotube-on-social-media.html
Anti ulcer drugs and their Advance pharmacology ||
Anti-ulcer drugs are medications used to prevent and treat ulcers in the stomach and upper part of the small intestine (duodenal ulcers). These ulcers are often caused by an imbalance between stomach acid and the mucosal lining, which protects the stomach lining.
||Scope: Overview of various classes of anti-ulcer drugs, their mechanisms of action, indications, side effects, and clinical considerations.
Title: Sense of Taste
Presenter: Dr. Faiza, Assistant Professor of Physiology
Qualifications:
MBBS (Best Graduate, AIMC Lahore)
FCPS Physiology
ICMT, CHPE, DHPE (STMU)
MPH (GC University, Faisalabad)
MBA (Virtual University of Pakistan)
Learning Objectives:
Describe the structure and function of taste buds.
Describe the relationship between the taste threshold and taste index of common substances.
Explain the chemical basis and signal transduction of taste perception for each type of primary taste sensation.
Recognize different abnormalities of taste perception and their causes.
Key Topics:
Significance of Taste Sensation:
Differentiation between pleasant and harmful food
Influence on behavior
Selection of food based on metabolic needs
Receptors of Taste:
Taste buds on the tongue
Influence of sense of smell, texture of food, and pain stimulation (e.g., by pepper)
Primary and Secondary Taste Sensations:
Primary taste sensations: Sweet, Sour, Salty, Bitter, Umami
Chemical basis and signal transduction mechanisms for each taste
Taste Threshold and Index:
Taste threshold values for Sweet (sucrose), Salty (NaCl), Sour (HCl), and Bitter (Quinine)
Taste index relationship: Inversely proportional to taste threshold
Taste Blindness:
Inability to taste certain substances, particularly thiourea compounds
Example: Phenylthiocarbamide
Structure and Function of Taste Buds:
Composition: Epithelial cells, Sustentacular/Supporting cells, Taste cells, Basal cells
Features: Taste pores, Taste hairs/microvilli, and Taste nerve fibers
Location of Taste Buds:
Found in papillae of the tongue (Fungiform, Circumvallate, Foliate)
Also present on the palate, tonsillar pillars, epiglottis, and proximal esophagus
Mechanism of Taste Stimulation:
Interaction of taste substances with receptors on microvilli
Signal transduction pathways for Umami, Sweet, Bitter, Sour, and Salty tastes
Taste Sensitivity and Adaptation:
Decrease in sensitivity with age
Rapid adaptation of taste sensation
Role of Saliva in Taste:
Dissolution of tastants to reach receptors
Washing away the stimulus
Taste Preferences and Aversions:
Mechanisms behind taste preference and aversion
Influence of receptors and neural pathways
Impact of Sensory Nerve Damage:
Degeneration of taste buds if the sensory nerve fiber is cut
Abnormalities of Taste Detection:
Conditions: Ageusia, Hypogeusia, Dysgeusia (parageusia)
Causes: Nerve damage, neurological disorders, infections, poor oral hygiene, adverse drug effects, deficiencies, aging, tobacco use, altered neurotransmitter levels
Neurotransmitters and Taste Threshold:
Effects of serotonin (5-HT) and norepinephrine (NE) on taste sensitivity
Supertasters:
25% of the population with heightened sensitivity to taste, especially bitterness
Increased number of fungiform papillae
Ozempic: Preoperative Management of Patients on GLP-1 Receptor Agonists Saeid Safari
Preoperative Management of Patients on GLP-1 Receptor Agonists like Ozempic and Semiglutide
ASA GUIDELINE
NYSORA Guideline
2 Case Reports of Gastric Ultrasound
These lecture slides, by Dr Sidra Arshad, offer a quick overview of physiological basis of a normal electrocardiogram.
Learning objectives:
1. Define an electrocardiogram (ECG) and electrocardiography
2. Describe how dipoles generated by the heart produce the waveforms of the ECG
3. Describe the components of a normal electrocardiogram of a typical bipolar leads (limb II)
4. Differentiate between intervals and segments
5. Enlist some common indications for obtaining an ECG
Study Resources:
1. Chapter 11, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 9, Human Physiology - From Cells to Systems, Lauralee Sherwood, 9th edition
3. Chapter 29, Ganong’s Review of Medical Physiology, 26th edition
4. Electrocardiogram, StatPearls - https://www.ncbi.nlm.nih.gov/books/NBK549803/
5. ECG in Medical Practice by ABM Abdullah, 4th edition
6. ECG Basics, http://www.nataliescasebook.com/tag/e-c-g-basics
These simplified slides by Dr. Sidra Arshad present an overview of the non-respiratory functions of the respiratory tract.
Learning objectives:
1. Enlist the non-respiratory functions of the respiratory tract
2. Briefly explain how these functions are carried out
3. Discuss the significance of dead space
4. Differentiate between minute ventilation and alveolar ventilation
5. Describe the cough and sneeze reflexes
Study Resources:
1. Chapter 39, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 34, Ganong’s Review of Medical Physiology, 26th edition
3. Chapter 17, Human Physiology by Lauralee Sherwood, 9th edition
4. Non-respiratory functions of the lungs https://academic.oup.com/bjaed/article/13/3/98/278874
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MANAGEMENT OF ATRIOVENTRICULAR CONDUCTION BLOCK.pdfJim Jacob Roy
Cardiac conduction defects can occur due to various causes.
Atrioventricular conduction blocks ( AV blocks ) are classified into 3 types.
This document describes the acute management of AV block.
Ethanol (CH3CH2OH), or beverage alcohol, is a two-carbon alcohol
that is rapidly distributed in the body and brain. Ethanol alters many
neurochemical systems and has rewarding and addictive properties. It
is the oldest recreational drug and likely contributes to more morbidity,
mortality, and public health costs than all illicit drugs combined. The
5th edition of the Diagnostic and Statistical Manual of Mental Disorders
(DSM-5) integrates alcohol abuse and alcohol dependence into a single
disorder called alcohol use disorder (AUD), with mild, moderate,
and severe subclassifications (American Psychiatric Association, 2013).
In the DSM-5, all types of substance abuse and dependence have been
combined into a single substance use disorder (SUD) on a continuum
from mild to severe. A diagnosis of AUD requires that at least two of
the 11 DSM-5 behaviors be present within a 12-month period (mild
AUD: 2–3 criteria; moderate AUD: 4–5 criteria; severe AUD: 6–11 criteria).
The four main behavioral effects of AUD are impaired control over
drinking, negative social consequences, risky use, and altered physiological
effects (tolerance, withdrawal). This chapter presents an overview
of the prevalence and harmful consequences of AUD in the U.S.,
the systemic nature of the disease, neurocircuitry and stages of AUD,
comorbidities, fetal alcohol spectrum disorders, genetic risk factors, and
pharmacotherapies for AUD.
Pulmonary Thromboembolism - etilogy, types, medical- Surgical and nursing man...VarunMahajani
Disruption of blood supply to lung alveoli due to blockage of one or more pulmonary blood vessels is called as Pulmonary thromboembolism. In this presentation we will discuss its causes, types and its management in depth.
ARTIFICIAL INTELLIGENCE IN HEALTHCARE.pdfAnujkumaranit
Artificial intelligence (AI) refers to the simulation of human intelligence processes by machines, especially computer systems. It encompasses tasks such as learning, reasoning, problem-solving, perception, and language understanding. AI technologies are revolutionizing various fields, from healthcare to finance, by enabling machines to perform tasks that typically require human intelligence.
Explore natural remedies for syphilis treatment in Singapore. Discover alternative therapies, herbal remedies, and lifestyle changes that may complement conventional treatments. Learn about holistic approaches to managing syphilis symptoms and supporting overall health.
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Genome in a bottle april 30 2015 hvp Leiden
1. genomeinabottle.org
Genome in a Bottle: You’ve
sequenced. How well did you do?
April 2015
Justin Zook, Marc Salit, and the Genome
in a Bottle Consortium
Presented by Steve Lincoln
6. genomeinabottle.org
Genome in a Bottle Consortium (GIAB)
Hosted by US National Institute of Standards and Technology
Goal: Provide infrastructure for
performance assessment of NGS
• Appropriately consented widely
available DNA samples, distributed
by the Coriell Institute
– Also, QCed Reference Material (RM)
versions from controlled lots will be
available from NIST
• High-accuracy reference data for
these samples
• Tools to facilitate their use
– With the Global Alliance Data
Working Group Benchmarking Team
ga4gh.org
7. genomeinabottle.org
GIAB Selected Samples
CEPH/Utah Pedigree 1463
✔
NA1288
9
NA12879
NA12890
NA12880
NA12881
NA12882
NA12883
NA12884
NA12885
NA12886
NA12887
NA12888
NA12893
NA12877 NA12878
NA12891 NA12892
✔ ✔
NA24149 NA24143
NA24385
Ashkenazi Jewish Trio
✔
NA24694 NA24695
NA24631
Asian (Han Chinese) Trio
✔
Note: Data from the complete families can be used to
improve variant calls in the specific GIAB samples.
New
New
Personal
Genome
Project
9. genomeinabottle.org
Goals for GIAB Data
• Close to 0 false positives
• Close to 0 false negatives (missing calls)
• Identify confident regions which have this high
accuracy
– Include as much of the genome as possible in the
confident regions (i.e. don’t just use the intersection set)
• Avoid bias towards any particular platform or
bioinformatics pipeline
– Leverage strengths of each individual platform
9Zook et al., Nature Biotechnology, 2014.
12. genomeinabottle.org
Integration Methods to Establish
Reference Variant Calls for NA12878
Candidate Variants from Each Platform
Identify Concordant/Discordant Variants
Identify Characteristics of Systematic Error
Arbitrate Using Evidence of Systematic Error
Determine Confidence Levels by Region
Zook et al., Nature Biotechnology, 2014.
13. genomeinabottle.org
Assigning confidence to genomic
regions for NA12878
High-confidence (77%)
• Platforms agree or we
understand the systematic
biases causing
disagreement
• At least some methods have
no evidence of systematic
errors
• Mendelian inheritance
consistent
Lower confidence (23%)
• In a region known to be
difficult for current
technologies
– Segmental Dups
– Repeats, Low Complexity
– High/Low GC
– Etc.
• Evidence of systematic error
across many platforms
• Inconsistent inheritance
Zook et al., Nature Biotechnology, 2014.
14. genomeinabottle.org
Assigning confidence to genomic
regions for NA12878
High-confidence (77%)
• Platforms agree or we
understand the systematic
biases causing
disagreement
• At least some methods have
no evidence of systematic
errors
• Mendelian inheritance
consistent
Lower confidence (23%)
• In a region known to be
difficult for current
technologies
– Segmental Dups
– Repeats, Low Complexity
– High/Low GC
– Etc.
• Evidence of systematic error
across many platforms
• Inconsistent inheritance
Zook et al., Nature Biotechnology, 2014.
A BED file of high confidence
regions is provided.
You should use it!
Really!
15. genomeinabottle.org
Quality Assessment of NA12878 Calls
in High-Confidence Regions
• 100% sensitivity/specificity vs. Get-RM data
– 427 SNPs and 42 indels, 366kb negative
• ≈99.8% Initial Sensitivity vs. Xprize Fosmid Sequences
– 135,652 SNVs and 10,942 insertions/deletions
– 124 SNPs and 37 indels (Sanger confirmed)
– After manual data review of discrepancies: >99.9%
• Most were errors were in the Fosmid data.
• Other QC
– Comparison vs SNP Microarrays
– Ti/Tv ratio
– Etc.
15Zook et al., Nature Biotechnology, 2014.
16. genomeinabottle.org
Quality Assessment of NA12878 Calls
in High-Confidence Regions
• 100% sensitivity/specificity vs. Get-RM data
– 427 SNPs and 42 indels, 366kb negative
• ≈99.8% Initial Sensitivity vs. Xprize Fosmid Sequences
– 135,652 SNVs and 10,942 insertions/deletions
– 124 SNPs and 37 indels (Sanger confirmed)
– After manual data review of discrepancies: >99.9%
• Most were errors were in the Fosmid data.
• Other QC
– Comparison vs SNP Microarrays
– Ti/Tv ratio
– Etc.
16Zook et al., Nature Biotechnology, 2014.
≈94,500 True+ SNVs
≈1400 True+ Indels
0 or 1 False+ or False–
(SNVs and indels together)
But ≈3 partial calls of complex
small variants
Per 120 MB*…
17. genomeinabottle.org
GeT-RM Browser from NCBI and CDC
• http://www.ncbi.nlm.nih.gov/variation/tools/get-rm/
• Allows visualization of data underlying call each call
18. genomeinabottle.org
NIST Human Genome
Reference Materials (RMs)
• NA12878 is available from
Coriell today
• NIST RM version will
available later in 2015
– DNA isolated from large
growth cell cultures
– Stable, homogeneous
– Best for regulated uses
• New AJ and Asian Samples
– Available for Coriell now
– NIST RM available in 2016
20. genomeinabottle.org
NGS Validation Process using
Genomes in Bottles
Sample
gDNA isolation
Library Prep
Sequencing
Alignment/Mapping
Variant Calling
Confidence Estimates
Downstream Analysis
Analytical Process
Genome in a Bottle Scope
Pre-Analytical Process
Clinical Interpretation
GIAB
Data
21. genomeinabottle.org
Uses of GIAB NA12878
Oncology – Molecular and Cellular Tumor Markers
“Next Generation” Sequencing (NGS) guidelines for
somatic genetic variant detection
www.bioplanet.com/gcat
22. genomeinabottle.org
• 7 Whole-Genomes Contributed 310 of 750 selected variants
– GIAB NA12878 and 6 others with similarly cleaned data
– 41% of the total set of variants came from 0.6% of the samples
• In 15 of 29 genes the 7 samples doubled (or more) the
selected variant count
• WCGs added variants in one gene (PTCH1) which otherwise
had none selected from clinical data
• Saved 310 Sanger confirmations
– Unlike confirmation, WCGs contribute both to sensitivity and
specificity measurements in a strong way
Contribution to Invitae Hereditary
Cancer Validation Study (29 genes)
Steve Lincoln, Geoff Nilsen, Shan Yang
23. genomeinabottle.org
• No coding variants in 5 of 29 genes
– CDKN2A, PALB2, RAD51C, SMAD4
– CHEK2 (a special case)
• Only 1 coding variant in 2 other genes
– PTEN, TP53
• The only errors in any reference data we
saw were in WGS data (but not GIAB!)
– 2 in NA19240, 1 in NA12892
– All errors in low-complexity sequence
• Many of the variants are repeated
– Partly due to using related individuals
– Partly because most are common
polymorphisms
Limitations of GIAB WCGs All Others
APC 31 9
ATM 26 10
BMPR1A 7 1
BRCA1 21 162
BRCA2 39 156
BRIP1 23 5
CDH1 12 4
CDKN2A 3
CHEK2 4
EPCAM 8 1
MEN1 18 1
MET 18 2
MLH1 4 6
MSH2 4 8
MSH6 11 7
MUTYH 4 23
NBN 16 3
PALB2 8
PALLD 6 1
PMS2 16 9
PTCH1 10
PTEN 1 1
RAD51C 4
RET 27 2
SMAD4 3
TP53 1 3
VHL 7 1
Steve Lincoln, Geoff Nilsen, Shan Yang
24. genomeinabottle.org
• No coding variants in 5 of 29 genes
– CDKN2A, PALB2, RAD51C, SMAD4
– CHEK2 (a special case)
• Only 1 coding variant in 2 other genes
– PTEN, TP53
• The only errors in any reference data we
saw were in WGS data (but not GIAB!)
– 2 in NA19240, 1 in NA12892
– All errors in low-complexity sequence
• Many of the variants are repeated
– Partly due to using related individuals
– Partly because most are common
polymorphisms
Limitations of GIAB
WCGs All Others
APC 31 9
ATM 26 10
BMPR1A 7 1
BRCA1 21 162
BRCA2 39 156
BRIP1 23 5
CDH1 12 4
CDKN2A 3
CHEK2 4
EPCAM 8 1
MEN1 18 1
MET 18 2
MLH1 4 6
MSH2 4 8
MSH6 11 7
MUTYH 4 23
NBN 16 3
PALB2 8
PALLD 6 1
PMS2 16 9
PTCH1 10
PTEN 1 1
RAD51C 4
RET 27 2
SMAD4 3
TP53 1 3
VHL 7 1
Steve Lincoln, Geoff Nilsen, Shan Yang
Genome in a Bottle is a valuable,
but not sufficient, part of a
validation study
25. genomeinabottle.org
The challenge in variant comparison: Complex
small variants have multiple representations
25
Ref: AAA CAGTGA GAA
Alt: AAA TCTCT GAA
hg19 NC_000001.10:114841792–114841797
27. genomeinabottle.org
The challenge in variant comparison: Complex
small variants have multiple representations
27
123456789-----012
Ref: AAACAGTGA-----GAA 4_9delCAGTGA
Alt: AAA------TCTCTGAA 9_10insTCTCT
123-456789012
Ref: AAA-CAGTGAGAA 3_4insT
|||-|--|::||| 5_6delAG
Alt: AAATC—-TCTGAA 8_9delGAinsCT
123456789012 4delA
Ref: AAACAGTGAGAA 4_6delCAGinsTC 5_6delAGinsTC
|||-::|::||| 8_9delGAinsCT 8_9delGAinsCT
Alt: AAA-TCTCTGAA
123456789012
Ref: AAACAGTGAGAA 4_9delCAGTGAinsTCTCT
|||:-:|::|||
Alt: AAAT-CTCTGAA
CG requires 2 reference bp
to separate variants
4C>T
5delA
6G>C
8_9delGAinsCT
28. genomeinabottle.org
The challenge in variant comparison: Complex
small variants have multiple representations
28
3insT
5_6delAG
8_9delGAinsCT
4_6delCAGinsTC
8_9delGAinsCT
4_9delCAGTGAinsTCTCT
4C>T
5delA
6G>C
8_9delGAinsCT
4delA
5_6delAGinsTC
8_9delGAinsCT
FP SNPs FP MNPs FP indels
Traditional
comparison
0.38%
(610)
100%
(915)
6.5%
(733)
Comparison
with allele
realignment
0.15%
(249)
4.2%
(38)
2.6%
(298)
Improved Comparison Tool in Development
by Kevin Jacobs of 23andme
Global Alliance Benchmarking Team
30. genomeinabottle.org
New Data for AJ and Asian Samples
Dataset Characteristics Coverage Availability Most useful for…
Illumina Paired-end Short read
150x150bp
~300x On FTP now SNPs/indels/some
SVs
Complete Genomics
Standard
Short read
26x26
~100x On FTP now SNPs/indels/some
SVs
Ion Proton Exome Short read
190bp average
~1000x On FTP now SNPs/indels in
exome
Illumina Mate- pair ~6kb insert size
150x150bp
~30x/individual Finished; on FTP
Apr 2015
SVs
Illumina “Moleculo” Synthetic Long
Reads
~30x long contigs Finished; on FTP
Apr-May 2015
SVs/phasing/assem
bly
Complete Genomics
LFR
Synthetic Long
Reads
~100x Finished; on FTP
Apr-May 2015
SNPs/indels/phasin
g
10X Synthetic Long
Reads
30-45x sequence Target May 2015 SVs/phasing/assem
bly
BioNano Genomics 200-250kbp optical
map fragments
~100x AJ individuals
~57x on Asian son
On FTP now SVs/assembly
PacBio ~10kb reads ~69x each child
~30x each parent
On FTP now SVs/phasing/assem
bly/STRs
31. genomeinabottle.org
Data Analysis Group – New Data Sets
Leaders
• Francisco de la Vega
– Annai Systems
• Chris Mason
– Weil Cornell Medical Center
• Tina Graves
– Washington University
• Valerie Schneider
– NCBI
Status
• Collecting Data into a
Central FTP Site
• Developing an Analysis Plan
• Developing a validation plan
and metrics
• Recruiting people to help
with the work.
This could be you.
We need volunteers!
32. genomeinabottle.org
Data Analysis Group – New Data Sets
Leaders
• Francisco de la Vega
– Annai Systems
• Chris Mason
– Weil Cornell Medical Center
• Tina Graves
– Washington University
• Valerie Schneider
– NCBI
Status
• Collecting Data into a
Central FTP Site
• Developing an Analysis Plan
• Developing a validation plan
and metrics
• Recruiting people to help
with the work.
This could be you.
We need volunteers!
Fame!
Glory!
Publications!
Free Data!
€ £ $
33. genomeinabottle.org
High-level analysis plan
Assembly
• Long reads
• Synthetic
long reads
• Mapping
• Integration
Small Variants
• Long reads
• Synthetic
long reads
• Short paired-
end
• Mate-pair
• Exome
• Integration
Personal
Genome
Reference for
Mapping
Phasing
• Long reads
• Synthetic
long reads
• Mapping
• Integration
SVs/VNTRs
• Long reads
• Synthetic
long reads
• Short paired-
end
• Mate-pair
• Mapping
• Integration
Phased,
Integrated, high-
confidence
variant calls
Francisco de la Vega
35. genomeinabottle.org
Acknowledgments
• FDA – Elizabeth Mansfield,
Computing staff
• Harvard School of Public Health
• GCAT website - David Mittelman,
Jason Wang
• Members of Genome in a Bottle
– New members welcome!
– Sign up on website for email
newsletters
Steering Committee
– Marc Salit
– Justin Zook
– David Mittelman
– Andrew Grupe
– Michael Eberle
– Steve Sherry
– Deanna Church
– Francisco De La Vega
– Christian Olsen
– Monica Basehore
– Lisa Kalman
– Christopher Mason
– Elizabeth Mansfield
– Liz Kerrigan
– Leming Shi
– Melvin Limson
– Alexander Wait Zaranek
– Nils Homer
– Fiona Hyland
– Steve Lincoln
– Don Baldwin
– Robyn Temple-Smolkin
– Chunlin Xiao
– Kara Norman
– Luke Hickey
36. genomeinabottle.org
For More Information
www.genomeinabottle.org
www.bioplanet.com/gcat - (old) comparison tool
www.ncbi.nlm.nih.gov/variation/tools/get-rm/ - Get-RM Browser
Global Alliance Benchmarking work group
– ga4gh.org/#/benchmarking-team
Twice yearly workshop
– Winter: at Stanford University, California, USA
– Summer (August 27-28) at NIST, Maryland, USA
• near Washington, DC
Open Meeting!
Justin Zook: jzook@nist.gov
Marc Salit: salit@nist.gov
Francisco de la Vega: francisco.dlv@gmail.com
Steve Lincoln: steve.lincoln@me.com