Detail program will be announced.

Date: June 14th-15th, 2023

Location: The Hilton Garden Inn Glasgow City Centre , Finnieston Quay, Glasgow, UK

Wednesday, June 14, 2023

8:45 a.m. Arrival

9:00 a.m. – 9:15 a.m. Opening remarks – Charles, Evan, Jan, Tobias

9.15 a.m. – 10.00 a.m. Data production update – Pille Hallast

Data management discussion

10:00 p.m. - 1:00 p.m. Updates from working groups. Moderator: Xander Arguello

1. Inversion breakpoints/SDs – David Porubsky

2. Chromosome Y – Pille Hallast

3. Transposable elements – Christine Beck/Berni Rodriguez-Martin

4. Functional analyses – Matthew Jensen/Mike Zody

1:00 p.m. – 2:00 p.m. Lunch

2:00 p.m. – 2:45 p.m. ONT sequencing of 1000 Genomes Project samples - Siegfried Schloissnig/David Porubsky

2:45 p.m. - 5:00 p.m. Discussions on:

1. Interactions with HPRC and other long-read sequencing efforts - Charles, Evan, Jan, Tobias,

David Porubsky

2. HGSVC3 paper discussions - Charles, Evan, Jan, Tobias

3. Production of variant call set

6:30 p.m. Group Dinner - Villa Toscana Restaurant, 1080 Argyle Street, Finnieston, Glasgow

Thursday, June 15, 2023

8:45 a.m. Arrival

9:00 a.m. - 11:45 a.m. Updates from working groups. Moderator: Xander Arguello

1. Single-sample Strand-seq Assembly Pipeline & Assembly production update - Mir

Henglin/Peter Ebert

2. Long-read based genome inference / genotyping - Samarendra Pani

3. SV discovery on graphs - Tobias Rausch, Arda Söylev

4. Accurate characterization of simple and complex SVs - Peter Audano

11:45 a.m. – 12:00 p.m. Closing remarks – Charles, Evan, Jan, Tobias

Date: October 24th, 2022

Location: JW Marriott Los Angeles L.A. Live, L.A.

Monday, October 24, 2022

8:45 a.m. Arrival at JW Marriott L.A.

9:00 a.m. – 9:15 a.m. Opening remarks – Charles, Evan, Jan, Tobias

9:15 a.m. – 10:00 a.m. HGSVC renewal general discussion – Charles, Evan, Jan, Tobias

Updates from the HPRC meeting

10:00 a.m.– 11:00 a.m. Data production plans for 2022/2023 - Pille Hallast

11:15 a.m. – 1:00 p.m. Updates from working groups/papers

1. SD genotyping and PSV detection – Timofey Prodanov

2. Chromosome Y – Pille Hallast

3. Inversions – David Porubsky

1:00 p.m. – 2:00 p.m. Lunch

2:00 p.m.– 4:00 p.m. Updates from working groups/papers

1. Transposable elements – Christine Beck

2. Complex SVs – Peter Audano

3. Functional analyses – Mindy Shi

4. VNTRs – Bida Gu

4:00 p.m.– 4:45 p.m. Discussions

4:45 p.m. – 5:00 p.m. Closing remarks – Charles, Evan, Jan, Tobias

6:30 p.m. Group Dinner: Le Grand Restaurant, 707 S. Grand Ave., L.A., CA. 90017

Date: May 3rd - 4th, 2022

Location: The University of Iceland, Reykjavik, Iceland

May 3rd, 2022

08:45 am Arrival at the University of Iceland Haskolatorg Building, Litla Torg Conf.

09:00 am – 09:15 am Opening remarks Charles, Evan, Jan, Tobias

09:15 am – 09:45 am HGSVC background & significance Charles, Evan, Jan, Tobias

09:45 am – 10:00 am IGSR update Sarah Hunt

10:00 am – 01:00 pm Working group summaries + relevance to renewal

1. Assemblies – Peter Ebert (10:00 – 10:25)

2. Inversions – David Porubsky (10:25 – 10:55) 10:55 – 11:10

Break

3. chrY – Pille Hallast (11:10 – 11:35)

4. Transposable elements – Christine Beck (11:35 – 12:00)

5. Complex SVs – Peter Audano (12:00 – 12:25)

6. Associations and genotyping – Tobias Marschall/Mindy Shi (12:25 – 12:50)

01:00 pm – 02:00 pm Lunch

02:00 pm – 03:00 pm Preliminary data presentations for renewal

1. Downsampling – William Harvey

2. Merging – Peter Audano

3. Pooled Strand-seq experiments –Celia Tsapalou

03:00 pm – 06:00 pm Renewal discussions: 2 rounds of breakouts regarding preparation of specific sections

o Aim 1 group – stays in Litla Torg

o Aim 2 group – Conference room HT-300

o Aim 3 group – Conference room O-104

o Aim 4 group – stays in Litla Torg

06:30 pm Group Dinner Fish Company, Vesturgata, 2A, 101 Reykjavik

May 4th, 2022

08:45 am Arrival at the University of Iceland Haskolatorg Building, Litla Torg Conf.

09:00 am – 12:00 pm Renewal discussions: 2 rounds of discussions/no formal presentation

o Aim 1 group – stays in Litla Torg

o Aim 2 group – Conference room HT-300

o Aim 3 group – Conference room O-106

o Aim 4 group – stays in Litla Torg

12:00 pm – 12:30 pm Data production, QC and data sharing update Scott Devine, Katy Munson, Patrick Hasenfeld, Pille Hallast, Peter Audano

12:30 pm – 01:00 pm Closing remarks Charles, Evan, Jan, Tobias

01:00 pm – 02:00 pm Lunch

Public Seminars on Human Genome Variation

02:00 pm – 02:30 pm “High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios” Mike Zody, the New York Genome Center

02:30 pm – 03:00 pm “Human Y chromosome – the full extent of genetic diversity within reach” Pille Hallast, The Jackson Laboratory

03:00 pm – 03:30 pm “Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders” David Porubsky, the University of Washington

October 4th, 2021, 10:00am-2:30pm EST 

10:00am - 10:10am Opening remarks Charles Lee, Evan Eichler, Jan Korbel and Tobias Marshall 

10:10am - 10:25am Yr2 data production, QC and data sharing Scott Devine, Katy Munson, Patrick Hasenfeld,

Qihui Zhu and Sarah Hunt 

10:25am - 10:45am Strand-seq and ONT-based methylation analyses Jan Korbel, Marc Jan Bonder and Rene Snajder 

10:45am - 11:00am Update on the on the assembly pipeline Peter Ebert 

11:00am - 11:15am A detailed analysis of gaps in HGSVC and HPRC assemblies David Porubsky 

11:15am - 11:30am Update on complex SVs Peter Audano, Jiadong Lin, Kai Ye and Christine Beck 

11:30am - 11:45am Analysis on the fragile VNTR sites Mark Chaisson 

11:45am - 12:00pm Evolution and functional impact of human MEIs The MEI group: Christine Beck, Scott Devine,

Ryan Mills, Arthur Zhou and Bernardo Rodríguez Martín etc 

12:00pm - 12:10pm Break 

12:10pm - 12:25pm Y chromosome analysis Pille Hallast 

12:25pm - 12:40pm Advances in (complex) SV genotyping Jana Ebler 

12:40pm - 12:55pm Genotyping and associations (eQTL and GWAS) The Functional group: Mindy Shi, Michael Zody

and Marc Jan Bonder etc 

12:55pm - 01:10pm Recurrent SV mutation analysis PingHsun Hsieh and Hufsah Ashraf 

01:10pm - 02:30pm Wrap up discussion and next steps Evan Eichler, Jan Korbel, Charles Lee and Tobias Marshall 

02:30pm - 04:30pm Executive session Jan Korbel, Tobias Marshall, Evan Eichler and Charles Lee 

May 3rd, 2021, 10:00am-2:30pm EST

10:10am - 10:25am Yr2 data production, QC and data release Katy Munson, Qihui Zhu, Patrick Hasenfeld

and Scott Devine

10:25am - 10:40am Assembly pipeline (PGAS) update and ONT scaffolding Peter Ebert

10:40am - 10:55am Variant merging William Harvey and Peter Audano

10:55am - 11:10am Human genome variation: VNTRs and SDs Mark Chaisson and Mitchell Vollger

11:10am - 11:20am Break

11:20am - 11:35am SV mechanism Peter Audano and Sushant Kumar

11:35am - 11:50am Inversion companion paper David Porubsky

11:50am - 12:05pm Evolution and functional impact of human MEIs Arthur Zhou and Bernardo Rodríguez Martín

12:05pm - 12:20pm Y chromosome and complex region analysis Pille Hallast and Feyza Yilmaz

12:20pm - 12:35pm Advances in (complex) SV genotyping Jana Ebler

12:35pm - 12:50pm Genotyping and associations (eQTL and GWAS) Michael Zody, Mindy Shi and Marc Jan Bonder

12:50pm - 01:00pm Break

01:00pm - 02:30pm Wrap up discussion, Yr3 data production and next steps Evan Eichler, Jan Korbel, Charles Lee

and Tobias Marshall

October 29th, 2020, 10:00 am - 2:30 pm EST: Manuscript discussion

09:30am - 09:40am Opening remarks Charles Lee, Evan Eichler and Jan Korbel

09:40am - 12:20pm HGSVC: Display items discussion

09:40am - 10:00am Fig 1: Methodology and Assembly Quality Peter Ebert, David Porubsky and Peter Audano

10:00am - 10:20am Fig 2: Haplotype-based SV Discovery Peter Audano

10:20am - 10:40am Fig 3a: SV Mechanisms. a) Inversion 16p11-12 region Ashley Sanders

10:40am - 11:00am Fig 3b: SV Mechanisms. b) MEI figures Scott Devine and Bernardo Rodríguez Martín

11:00am - 11:20am Fig 3c: Complex Structural Variants Alex Hastie, Joyce Lee and Feyza Yilmaz                

11:20am - 11:40am Fig 4a: Genotyping into the 1000G data Michael Zody, Jana Ebler and Tobias Marschall

11:40am - 12:00pm Fig 4b: Ancestry informative PingHsun Hsieh, Rebecca Serra Mari and Tobias Marschall

12:00pm - 12:20pm Fig 4c: GWAS, eQTL analyses Arvis Sulovari, Mindy Shi, Marc Jan Bonder and Oliver Stegle

12:20pm - 12:30pm Break

12:30pm - 02:00pm 1000G manuscript discussion Michael Zody

02:00pm - 02:30pm Day 1 wrap up discussion Evan Eichler, Jan Korbel and Charles Lee

October 30th, 2020, 10:00 am - 2:30 pm EST: HGSVC strategy meeting

10:00am - 10:15am HGSVC Year 2 data production, QC and release Katy Munson, Qihui Zhu, Scott Devine

and Susan Fairley

10:15am - 02:15pm HGSVC strategy planning: new manuscripts and funding Jan Korbel, Charles Lee and Evan Eichler

02:15pm - 02:30pm Day 2 wrap up discussion Charles Lee, Evan Eichler and Jan Korbel 

May 4th, 2020, 9:30 am - 10:00 am EST: Pre-meeting

09:30am - 10:00am Pre-meeting: Data management Susan Fairley

May 4th, 2020, 10:00 am - 2:30 pm EST: All-hands meeting

10:00am - 10:10am Opening remarks Charles Lee, Evan Eichler and Jan Korbel

10:10am - 10:20am Data production, QC and release Susan Fairley, Katy Munson, Peter Audano, Qihui Zhu

and Scott Devine

10:20am - 10:50am Phased genome assembly Peter Ebert

10:50am - 11:20am Variant discovery with phased assemblies Peter Audano

11:20am - 11:50am Assembly validation and variant calling Mark Chaisson

11:50am - 12:20pm Structural variant calling using long-reads Tobias Rausch

12:20pm - 12:30pm Break

12:30pm - 01:00pm Inversion analysis Ashley Sanders, David Porubsky

01:00pm - 01:30pm MEI update

01:00pm - 01:25pm MEI discovery in HG00514 CLR and CCS assemblies  Scott Devine

01:25pm - 01:30pm Mobilome profiling with MEIGA at HGSVC2 dataset  Bernardo Rodriguez-Martin

01:30pm - 02:30pm Day 1 wrap up discussion Jan Korbel, Evan Eichler and Charles Lee

May 5th, 2020, 10:00 am - 2:40 pm EST

10:00am - 11:00am Genotyping

10:00am - 10:30am Graph-based genotyping of SVs Jana Ebler, Tobias Marschall

10:30am - 11:00am Genotyping and phasing accuracy for structural variants Michael Zody

11:00am - 11:30am Bionano genome imaging for discovery, confirmation, QC  and scaffolding Alex Hastie

11:30am - 12:30pm Population-specific biology

11:30am - 12:00pm Ancestry reconstruction Rebecca Serra Mari, Tobias Marschall

12:00pm - 12:30pm Local ancestry inference for complete phased genomes PingHsun Hsieh

12:30pm - 12:40pm Break

12:40pm - 01:40pm Day 2 wrap up discussion Evan Eichler, Charles Lee and Jan Korbel

01:40pm - 02:40pm HGSVC next steps Charles Lee, Evan Eichler and Jan Korbel