Update on Hearing Loss CDWG Curation Efforts

This update provides details on the goals and members of the Hearing Loss Clinical Domain Working Group (CDWG). The group aims to facilitate gene and variant curation for hearing loss, utilizing expert reviews and collaborating with resources globally. Key activities include gene curation, variant classification, and outreach to enhance knowledge sharing and submissions to databases like ClinVar. With an extensive roster of expert members, the CDWG implements a comprehensive strategy to curate evidence for gene-disease relationships, standardize variant classification guidelines, and maintain clinical validity schemes. The included images highlight the group members, goals, and gene curation strategy in detail.

• Hearing Loss
• CDWG
• Gene Curation
• Variant Classification
• Data Submission

pre_t Follow

Uploaded on Feb 20, 2025 | 0 Views

Download Presentation

Please find below an Image/Link to download the presentation.

The content on the website is provided AS IS for your information and personal use only. It may not be sold, licensed, or shared on other websites without obtaining consent from the author. Download presentation by click this link. If you encounter any issues during the download, it is possible that the publisher has removed the file from their server.

Presentation Transcript

1. Hearing Loss CDWG Curation Update Biocurator Call 5.11.17 Marina DiStefano, Ph.D. Sarah Hemphill, B.S. Brandon Cushman, B.S.

2. Goals of the HL CDWG 1. Outreach a) Identify experts and resources around the globe b) Facilitate submission of existing variants into ClinVar 2. Gene Curation a) Curate evidence for gene-disease relationships b) Use ClinGen s clinical validity scheme 3. Variant Curation a) Modify existing ACMG guidelines for variant classification specifically for hearing loss and the associated genes b) Resolve discrepancies in existing variant classifications in ClinVar c) Review variants for expert classification (prioritize most common)

3. Working Group Members Expanded Expert Membership (quarterly calls) Subcommittee Working Group (biweekly calls) Alexander Chapin, PhD Amy Hernandez, MS, CGC Arti Pandya, MD, MBA Cynthia Morton, PhD Elizabeth Black- Ziegelbein Hannie Kremer, PhD Hatice Duzkale, MD, MPH, PhD Hela Azaiez, PhD Hideki Mutai, PhD Ignacio del Castillo, PhD John Alexander, PhD Jun Shen, PhD Karen Avraham, PhD Kevin Booth Margaret Kenna, MD, MPH Miguel Moreno Pelayo, PhD Sonia Abdelhak, PhD Tatsuo Matsunaga, MD, PhD Wenying Zhang, PhD Andrew Griffith, MD, PhD Anne Giersch, PhD Byung Yoon Choi, PhD Christine Petit, MD, PhD Diana Kolbe, PhD Guy Van Camp, PhD Hui-Jun Yuan, PhD Ian Krantz, MD Jeffrey Holt, PhD Jessica Ratay, MS, CGC John Greinwald, MD Kazuki Yamazawa MD., Ph.D. Kejian Zhang, MD, MBA Lilian Downie, PhD Lisbeth Tranebjaerg, MD, PhD Lucas Bronicki, PhD Makoto Hosoya MD., Ph.D. Mat as Mor n, PhD Mustafa Tekin, MD Parna Chatteraj Rachel Burt, PhD Richard Smith, MD Rong Mao, MD Saber Masmoudi, PhD Sean Ephraim We have 58 members at 26 institutions across 5 continents Shin-ichi Usami, MD, PhD Suzanne Leal, PhD Tao Yang, PhD Thomas Friedman, PhD Un-Kyung Kim, PhD Xue Liu, PhD Zippi Brownstein, PhD WG Chairs: Ahmad Abou Tayoun, PhD Sami Amr, PhD Heidi Rehm, PhD WG Coordinator: Andrea Oza, MS, CGC Senior Biocurator Marina DiStefano, PhD Staff Biocurators: Sarah Hemphill Brandon Cushman

4. HL Gene Curation Strategy Solicit via sign-up from the group. cannot be gene discoverer Expert Review Primary Biocurator Content Curator (Expertise in Hearing Loss domain) (Expertise in ClinGen framework) (Bring to CDWG for discussion and vote) Primary Clinical Validity Classification Finalize Clinical Validity Classification

5. HL Gene Curation ClinGen Personnel Content Curators Biocurators Ahmad Abou Tayoun, Ph.D., FACMG Sami Amr, Ph.D., FACMG Andrea Oza, M.S., CGC Marina DiStefano, Ph.D. Sarah Hemphill Brandon Cushman Tatsuo Matsunaga, MD, Ph.D. Wenying Zhang, Ph.D., FACMG Alex Chapin, Ph.D. Jun Shen, Ph.D., FACMG Hela Azaeiz, Ph.D. Hatice Duzkale, MD Ph.D. MPH FACMG Kevin Booth We have 13 members across 6 institutions

6. HL Current Curation Progress 4 (4%) 90 gene:disease pairs curated 35 content reviewed 17 expert- approved (on website) Conflicting/None 16 (18%) Limited 40 (44%) Moderate Strong 24 (27%) Definitive 6 (7%) Syndromic 32% Nonsyndr omic 68%

7. Lessons Learned: OPTIMIZING CURATION FOR GENETIC HEARING LOSS

8. Challenge #1 Hearing loss is a highly heterogeneous condition >400 genes may be associated with syndromic hearing loss 100 genes associated with nonsyndromic hearing loss (Abou Tayoun et al 2016 PMID: 26562227) How do we prioritize gene curations?

9. Challenge #2 > 400 genes are associated with syndromic hearing loss. Some of these are syndromes where hearing loss is minor phenotype. How do we evaluate which syndromes to curate? The group decided to tackle curation with the aim of designing hearing loss panels in mind.

10. Solution #2: Rapid Triage Solution #1: Gene Curation Prioritization Rapid Triage Questions Gene Inheritance Disease Is disease syndromic? PHASE 1: Proof of Principle 18 definitive Hearing Loss genes PHASE 2: Rapid Curation Triage Exercise (GTR HL Genes) Clinical Presentation Hearing Loss Genes on 1 test in GTR (~170 genes) First paper reported Number of HGMD hits Variant Spectrum General Notes PHASE 3: HL Curation Gene Prioritization Curate limited genes first (nonsyndromic clinical presentation) Rapid clinical validity classification

11. Challenge #3 Many hearing loss genes are associated with multiple (syndromic and nonsyndromic) presentations Of the ~170 genes we triaged, 22 have more than one disease association How can we maximize content curation efficiency? Solution #3: Give content reviewers all associations for each assigned gene (to save literature search time)

12. Challenge #4 The large number of gene curations stretches the bandwidth of our Content Curators How do we make the most of our volunteer force? We decided to ask content curators to only review moderate/limited/other genes.

13. Solution #4: Curation decision tree Primary Curation Clinical Validity: Moderate/Limited/ Clinical Validity: Definitive/Strong *Gene curations are presented to the HL CDWG sub-committee (~15 experts on an average call) Other Rapid Presentation and voting by CDWG* Content Curation Full Presentation and voting by CDWG*

14. Expert-requested curation additions Experts requested additional information in our presentations: Requests differed based on field of expertise Examples include: Transcript information All proposed disease associations for gene Variant spectrum (ClinVar, HGMD)

15. Ongoing Projects Gene Curation Blurbs Pre-curation documentation (with other ClinGen curators)

16. GENE CURATION EXAMPLES

17. DIAPH1: Sensorineural HL and macrothrombocytopenia Autosomal dominant First reported in 1997 in large Costa Rican family segregating apparently nonsyndromic HL (78 affecteds had variant, no non-segregations) Scored only 4 other papers, all from 2016 2 of these report novel phenotype, macrothrombocytopenia, which perfectly segregated with HL phenotype (3 variant points, 6 segregation points) Macrothrombocytopenia Platelet disorder, in which platelets are enlarged and reduced in number Can be mild and thus subclinical Original 1997 family was not tested Experimental evidence Drosophila model with het. null mutation had no auditory function, DIAPH1 promoter is activated by MITF, cell culture model had microvilli elongation and congestion, Heterozygous mouse model with patient variant had progressive HL Points maxed at 6 Lump or split? Definitive for HL phenotype, but blood phenotype first reported only in 2016

18. USH1C: Usher syndrome type I (autosomal recessive) Genetic evidence Verpy 2000 (10973247) Consanguineous Lebanese family with LOF variant: 6 points Bitner-Glindzicz 2000 (10973248) Two consanguineous families with 122kb deletion including part of USH1C: 5 points DeAngelis 2001 (11239869) Consanguineous American family of Lebanese descent, same variant as family in Verpy 2000: 3 points (segregation only) Aparisi 2010 (21203349) Two non-consanguineous families with homozygous LOF variants: 4 points Genetic evidence maxed Experimental evidence Johnson 2003 (14519688) Deaf circler mouse has 12kb deletion in USH1C, profound deafness and vestibular dysfunction, no retinal phenotype: 1 point Boeda 2002 (12485990) Harmonin interacts with F-actin, cadherin 23, and myosin VIIa: 0.5 points Adato 2004 (15590703) Harmonin interacts with protocadherin 15 and sans: 0.5 points Lentz 2010 (20095043) Knock-in mouse model generated (originally reported in Lentz 2007) with human splice mutation c.216G>A. First mouse model of Usher type I to develop both deafness and retinal phenotypes: 2 points Antisense oligos blocked altered splicing in mice with c.216G>A mutation (seen in humans), and rescued hearing: 2 points Gregory 2013 (23613530) Harmonin enhances calcium channel that regulates IHC exocytosis and synaptic transduction: 0.5 points Sahly 2012 (23045546) Colocalization of harmonin, cadherin-23, protocadherin-15, sans in macaque photoreceptor cells: 0.5 points Experimental evidence maxed DEFINITIVE

19. ADCY1: Sensorineural hearing loss (AR) Experimental evidence Santos-Cortez et al. 2014 (24482543) Two knockdown zebra fish models were generated (one with each isoform of ADCY1: a and b). Both had morphological defects, but only the ADCY1b KD fish had loss of startle response. (1pt due to different gene structure) ADCY1 was expressed in mouse temporal bones during all developmental stages. IF demonstrated it localized to IHCs, pillar cells, OHCs, and supporting cells. Rat expression was similar (0.5pts) The p.Arg1038Ter variant was transfected into Cos7 cells and the variant was not degraded, but mislocalized from the microvillar and lateral plasma membrane. Authors propose that c-terminal truncation can affect localization in actin- based microvilli and stereocilia. (0.5pts) Content reviewed 3/13/17: Moderate, 10 pts Reviewed by CDWG 5/10/17: LIMITED Genetic evidence Santos-Cortez et al. 2014(24482543) WES, NM_021116.2(ADCY1):c.3112C>T (p.Arg1038Ter) (8pts) Variant is in last exon, absent from gnomAD Consanguineous Pakistani family. Published LOD is 5.8. Pre-lingual onset, mild to moderate hearing loss. One had asymmetric HL with profound HL in worse ear. HL was determined to be mixed sensorineural and conductive 8 points, genetic evidence 2 points, experimental evidence Limited 1-6 Moderate 7-11

20. ADCY1 Mouse Model Welker et al 1996: barrelless (brl) mouse (spontaneous retrotransposon insertion into ADCY1 gene) Homozygous brl mice and separate ADCY1 KO mice were largely evaluated for neurological disturbances Altered distribution of somatosensory cortex (barrel-wall neurons) Wei et al 2002: No differences from WT mice in response to acute pain Reduced behavioral responses to inflammatory stimuli Tremblay et al 2002: No functional loss in short and long-term latency auditory evoked responses (Santos-Cortez et al claim that this may not be a reliable measurement for moderate cochlear loss) Lu et al 2003: brl mice have decreased functional AMPA receptors Disruption in PKA signaling (potentially calcium influx)

21. DNMT1: DNMT1 methylopathy Autosomal dominant Historically two separate disorders (Hereditary sensory neuropathy and Autosomal dominant cataplexy, ataxia, deafness and narcolepsy) Later considered to be one disorder Due to earlier onset/more severe presentation of other symptoms, should this gene be on HL panels?

22. DNMT1: DNMT1 Methylopathy REVIEWED 2/10/17: DEFINITIVE Experimental evidence Kernohan et al. 2016 (PMID 27602171) Identified a significant increase in the methylation of GPR176 promotor in patient cells (1 point) Klein et al. 2011 (PMID 21532572) Expressed mutant proteins found in patients in E. coli cells and performed stability and localization studies on the proteins (2 points) Also investigated the effect on methylation of the DNA of the variants (1 point) Sun et al. 2014 (PMID 25033457) Investigated the genome methylation profiles of matched sibling pairs one with the Y495C variant and one w/o (1 point) Genetic evidence Winkelmann et al. 2012 (PMID 22328086) 4 probands; 4 segregations (4.5 points) Pedroso et al. 2013 (PMID 23904686) 1 proband; 0 segregations (2 points) Kernohan et al. 2016 (PMID 27602171) 1 proband; 0 segregations (0.5 points) Kaveh et al. 2014 (PMID 24727570) 2 proband; 0 segregations (2 points) Klein et al. 2011 (PMID 21532572) 4 probands; 15 segregations (9 points)*

23. BSND: Bartter Syndrome and ARNSHL Autosomal recessive LoF mechanism of disease (Bartter Syndrome) Missense variants (ARNSHL) Pakistani founder mutation KO mouse is embryonic lethal Conditional KO exists for inner ear

24. BSND: Bartter Syndrome Experimental Evidence Birkenhager et al. 2001 (PMID 11687798) The BSND gene was strongly expressed in the murine kidney and in the stria vascularis of the inner ear. (0.5 points) Waldegger et al. 2002 (PMID 12111250) Both the BSND gene and the proteins it modifies are expressed in the rat nephron. (0.5 points) ClC-K1, ClC-Ka, and ClCKb (Bartter proteins) proteins selectively immunoprecipitated with barttin. (0.5 points) Barttin was shown to be a protein modifier of the ClC-K proteins (which are associated with Bartter syndrome) by increasing the current and voltage potential of Xenopus oocytes expressing both barttin and ClC-K. (0.5 points) The p.Arg8Leu and p.Arg8Trp variants completely abolished ClC-K activation. The p.Gly10Ser variant had no affect on ClC-K activation. (0.5 points) Estevez et al. 2001 (PMID 11734858) All truncating variants showed a significant decrease in cell conductance when compared to the WT. Any truncating variants at or before residue 85 abolished protein function. All missense variants tested significantly decreased cell conductance with the exception of p.Gly10Ser which increased cell conduction. (0.5 points) Rickheit et al. 2008 (PMID 18833191) KO mice exhibited a 60dB hearing loss compared to controls. The KO mice showed a drop in endocochlear potential in cochlear hair cells. Outer hair cells in KO mice began degrading after a few weeks and progressively degraded until they were completely lost. (2 points) Janssen et al. 2009 (PMID 18776122) This paper studied the effects of known mutations in BSND on the function and localization of the barttin protein. (1 point) REVIEWED 3/13/17: DEFINITIVE Genetic Evidence Birkenhager et al. 2001 (PMID 11687798) 5 probands; 3 segregations (11 points) Miyamura et al. 2003 (PMID 12574213) 1 proband; 0 segregations (1 point) 12 points, genetic evidence 6 points, experimental evidence >3 years across publications Definitive (12-18 points)

25. BSND: ARNSHL REVIEWED 3/13/17: MODERATE Genetic Evidence Riazzuddin et al. 2009 (PMID 19646679) 4 probands; 36 segregations (19 points) Iqbal et al. 2011 (PMID 21541222) 1 proband; 6 segregations (5 points) Shafique et al. 2014 (PMID 24949729) 1 proband; 5 segregations (5 points) Miyagawa et al. 2013 (PMID 23967202) 1 proband; no segregations (0 points) Experimental Evidence Riazzuddin et al. 2009 (PMID 19646679) This study expressed WT and I12T barttin with ClC-Ka and ClC-Kb in HEK293T cells and measured ion currents through the cells using a patch-clamp method. Current amplitudes in cells expressing I12T were significantly lower than for WT expressing cells. (0.5 points) Rickheit et al. 2008 This study created a conditional KO mouse for the BSND gene where the gene was only knocked out in the inner ear but not in the kidney. The KO mice exhibited a 60dB hearing loss compared to controls. (2 points) 9 points, genetic evidence 2.5 points, experimental evidence >3 years across publications Definitive (12-18 points)