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2. Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy

Author

O’Donnell-Luria, Anne H, Pais, Lynn S, Faundes, Víctor, Wood, Jordan C, Sveden, Abigail, Luria, Victor, Jamra, Rami Abou, Accogli, Andrea, Amburgey, Kimberly, Anderlid, Britt Marie, Azzarello-Burri, Silvia, Basinger, Alice A, Bianchini, Claudia, Bird, Lynne M, Buchert, Rebecca, Carre, Wilfrid, Ceulemans, Sophia, Charles, Perrine, Cox, Helen, Culliton, Lisa, Currò, Aurora, Study, Deciphering Developmental Disorders, McRae, Jeremy F, Clayton, Stephen, Fitzgerald, Tomas W, Kaplanis, Joanna, Prigmore, Elena, Rajan, Diana, Sifrim, Alejandro, Aitken, Stuart, Akawi, Nadia, Alvi, Mohsan, Ambridge, Kirsty, Barrett, Daniel M, Bayzetinova, Tanya, Jones, Philip, Jones, Wendy D, King, Daniel, Krishnappa, Netravathi, Mason, Laura E, Singh, Tarjinder, Tivey, Adrian R, Ahmed, Munaza, Anjum, Uruj, Archer, Hayley, Armstrong, Ruth, Awada, Jana, Balasubramanian, Meena, Banka, Siddharth, Baralle, Diana, Barnicoat, Angela, Batstone, Paul, Baty, David, Bennett, Chris, Berg, Jonathan, Bernhard, Birgitta, Bevan, A Paul, Bitner-Glindzicz, Maria, Blair, Edward, Blyth, Moira, Bohanna, David, Bourdon, Louise, Bourn, David, Bradley, Lisa, Brady, Angela, Brent, Simon, Brewer, Carole, Brunstrom, Kate, Bunyan, David J, Burn, John, Canham, Natalie, Castle, Bruce, Chandler, Kate, Chatzimichali, Elena, Cilliers, Deirdre, Clarke, Angus, Clasper, Susan, Clayton-Smith, Jill, Clowes, Virginia, Coates, Andrea, Cole, Trevor, Colgiu, Irina, Collins, Amanda, Collinson, Morag N, Connell, Fiona, Cooper, Nicola, Cresswell, Lara, Cross, Gareth, Crow, Yanick, D’Alessandro, Mariella, Dabir, Tabib, Davidson, Rosemarie, Davies, Sally, de Vries, Dylan, Dean, John, Deshpande, Charu, Devlin, Gemma, Dixit, Abhijit, and Dobbie, Angus

Subjects
Biological Sciences, Genetics, Autism, Neurosciences, Brain Disorders, Neurodegenerative, Intellectual and Developmental Disabilities (IDD), Pediatric, Clinical Research, Epilepsy, Mental Health, Aetiology, 2.1 Biological and endogenous factors, Neurological, Adolescent, Adult, Child, Child, Preschool, DNA-Binding Proteins, Female, Genetic Variation, Haploinsufficiency, Heterozygote, Humans, Infant, Male, Neurodevelopmental Disorders, Pedigree, Phenotype, Young Adult, Deciphering Developmental Disorders (DDD) Study, H3K4 methylation, KMT2E, autism, epilepsy, epileptic encephalopathy, global developmental delay, intellectual disability, neurodevelopmental disorder, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

We delineate a KMT2E-related neurodevelopmental disorder on the basis of 38 individuals in 36 families. This study includes 31 distinct heterozygous variants in KMT2E (28 ascertained from Matchmaker Exchange and three previously reported), and four individuals with chromosome 7q22.2-22.23 microdeletions encompassing KMT2E (one previously reported). Almost all variants occurred de novo, and most were truncating. Most affected individuals with protein-truncating variants presented with mild intellectual disability. One-quarter of individuals met criteria for autism. Additional common features include macrocephaly, hypotonia, functional gastrointestinal abnormalities, and a subtle facial gestalt. Epilepsy was present in about one-fifth of individuals with truncating variants and was responsive to treatment with anti-epileptic medications in almost all. More than 70% of the individuals were male, and expressivity was variable by sex; epilepsy was more common in females and autism more common in males. The four individuals with microdeletions encompassing KMT2E generally presented similarly to those with truncating variants, but the degree of developmental delay was greater. The group of four individuals with missense variants in KMT2E presented with the most severe developmental delays. Epilepsy was present in all individuals with missense variants, often manifesting as treatment-resistant infantile epileptic encephalopathy. Microcephaly was also common in this group. Haploinsufficiency versus gain-of-function or dominant-negative effects specific to these missense variants in KMT2E might explain this divergence in phenotype, but requires independent validation. Disruptive variants in KMT2E are an under-recognized cause of neurodevelopmental abnormalities.

Published
2019

3. Recommendations for clinical interpretation of variants found in non-coding regions of the genome

Author

Ellingford, Jamie M., Ahn, Joo Wook, Bagnall, Richard D., Baralle, Diana, Barton, Stephanie, Campbell, Chris, Downes, Kate, Ellard, Sian, Duff-Farrier, Celia, FitzPatrick, David R., Greally, John M., Ingles, Jodie, Krishnan, Neesha, Lord, Jenny, Martin, Hilary C., Newman, William G., O’Donnell-Luria, Anne, Ramsden, Simon C., Rehm, Heidi L., Richardson, Ebony, Singer-Berk, Moriel, Taylor, Jenny C., Williams, Maggie, Wood, Jordan C., Wright, Caroline F., Harrison, Steven M., and Whiffin, Nicola

Published
2022
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5. Advanced variant classification framework reduces the false positive rate of predicted loss of function (pLoF) variants in population sequencing data

Author

Singer-Berk, Moriel, primary, Gudmundsson, Sanna, additional, Baxter, Samantha, additional, Seaby, Eleanor G, additional, Wood, Jordan C, additional, Son, Rachel G, additional, Watts, Nicholas A, additional, Karczewski, Konrad, additional, Harrison, Steven, additional, MacArthur, Daniel G, additional, Rehm, Heidi L, additional, and O'Donnell-Luria, Anne, additional

Published
2023
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6. Centers for Mendelian Genomics: A decade of facilitating gene discovery

Author

Baxter, Samantha M., primary, Posey, Jennifer E., additional, Lake, Nicole J., additional, Sobreira, Nara, additional, Chong, Jessica X., additional, Buyske, Steven, additional, Blue, Elizabeth E., additional, Chadwick, Lisa H., additional, Coban-Akdemir, Zeynep H., additional, Doheny, Kimberly F., additional, Davis, Colleen P., additional, Lek, Monkol, additional, Wellington, Christopher, additional, Jhangiani, Shalini N., additional, Gerstein, Mark, additional, Gibbs, Richard A., additional, Lifton, Richard P., additional, MacArthur, Daniel G., additional, Matise, Tara C., additional, Lupski, James R., additional, Valle, David, additional, Bamshad, Michael J., additional, Hamosh, Ada, additional, Mane, Shrikant, additional, Nickerson, Deborah A., additional, Rehm, Heidi L., additional, O’Donnell-Luria, Anne, additional, Adams, Marcia, additional, Aguet, François, additional, Akay, Gulsen, additional, Anderson, Peter, additional, Antonescu, Corina, additional, Arachchi, Harindra M., additional, Atik, Mehmed M., additional, Austin-Tse, Christina A., additional, Babb, Larry, additional, Bacus, Tamara J., additional, Bahrambeigi, Vahid, additional, Balasubramanian, Suganthi, additional, Bayram, Yavuz, additional, Beaudet, Arthur L., additional, Beck, Christine R., additional, Belmont, John W., additional, Below, Jennifer E., additional, Bilguvar, Kaya, additional, Boehm, Corinne D., additional, Boerwinkle, Eric, additional, Boone, Philip M., additional, Bowne, Sara J., additional, Brand, Harrison, additional, Buckingham, Kati J., additional, Byrne, Alicia B., additional, Calame, Daniel, additional, Campbell, Ian M., additional, Cao, Xiaolong, additional, Carvalho, Claudia, additional, Chander, Varuna, additional, Chang, Jaime, additional, Chao, Katherine R., additional, Chinn, Ivan K., additional, Clarke, Declan, additional, Collins, Ryan L., additional, Cummings, Beryl, additional, Dardas, Zain, additional, Dawood, Moez, additional, Delano, Kayla, additional, DiTroia, Stephanie P., additional, Doddapaneni, Harshavardhan, additional, Du, Haowei, additional, Du, Renqian, additional, Duan, Ruizhi, additional, Eldomery, Mohammad, additional, Eng, Christine M., additional, England, Eleina, additional, Evangelista, Emily, additional, Everett, Selin, additional, Fatih, Jawid, additional, Felsenfeld, Adam, additional, Francioli, Laurent C., additional, Frazar, Christian D., additional, Fu, Jack, additional, Gamarra, Emmanuel, additional, Gambin, Tomasz, additional, Gan, Weiniu, additional, Gandhi, Mira, additional, Ganesh, Vijay S., additional, Garimella, Kiran V., additional, Gauthier, Laura D., additional, Giroux, Danielle, additional, Gonzaga-Jauregui, Claudia, additional, Goodrich, Julia K., additional, Gordon, William W., additional, Griffith, Sean, additional, Grochowski, Christopher M., additional, Gu, Shen, additional, Gudmundsson, Sanna, additional, Hall, Stacey J., additional, Hansen, Adam, additional, Harel, Tamar, additional, Harmanci, Arif O., additional, Herman, Isabella, additional, Hetrick, Kurt, additional, Hijazi, Hadia, additional, Horike-Pyne, Martha, additional, Hsu, Elvin, additional, Hu, Jianhong, additional, Huang, Yongqing, additional, Hurless, Jameson R., additional, Jahl, Steve, additional, Jarvik, Gail P., additional, Jiang, Yunyun, additional, Johanson, Eric, additional, Jolly, Angad, additional, Karaca, Ender, additional, Khayat, Michael, additional, Knight, James, additional, Kolar, J. Thomas, additional, Kumar, Sushant, additional, Lalani, Seema, additional, Laricchia, Kristen M., additional, Larkin, Kathryn E., additional, Leal, Suzanne M., additional, Lemire, Gabrielle, additional, Lewis, Richard A., additional, Li, He, additional, Ling, Hua, additional, Lipson, Rachel B., additional, Liu, Pengfei, additional, Lovgren, Alysia Kern, additional, López-Giráldez, Francesc, additional, MacMillan, Melissa P., additional, Mangilog, Brian E., additional, Mano, Stacy, additional, Marafi, Dana, additional, Marosy, Beth, additional, Marshall, Jamie L., additional, Martin, Renan, additional, Marvin, Colby T., additional, Mawhinney, Michelle, additional, McGee, Sean, additional, McGoldrick, Daniel J., additional, Mehaffey, Michelle, additional, Mekonnen, Betselote, additional, Meng, Xiaolu, additional, Mitani, Tadahiro, additional, Miyake, Christina Y., additional, Mohr, David, additional, Morris, Shaine, additional, Mullen, Thomas E., additional, Murdock, David R., additional, Murugan, Mullai, additional, Muzny, Donna M., additional, Myers, Ben, additional, Neira, Juanita, additional, Nguyen, Kevin K., additional, Nielsen, Patrick M., additional, Nudelman, Natalie, additional, O’Heir, Emily, additional, O’Leary, Melanie C., additional, Ongaco, Chrissie, additional, Orange, Jordan, additional, Osei-Owusu, Ikeoluwa A., additional, Paine, Ingrid S., additional, Pais, Lynn S., additional, Paschall, Justin, additional, Patterson, Karynne, additional, Pehlivan, Davut, additional, Pelle, Benjamin, additional, Penney, Samantha, additional, Perez de Acha Chavez, Jorge, additional, Pierce-Hoffman, Emma, additional, Poli, Cecilia M., additional, Punetha, Jaya, additional, Radhakrishnan, Aparna, additional, Richardson, Matthew A., additional, Rodrigues, Eliete, additional, Roote, Gwendolin T., additional, Rosenfeld, Jill A., additional, Ryke, Erica L., additional, Sabo, Aniko, additional, Sanchez, Alice, additional, Schrauwen, Isabelle, additional, Scott, Daryl A., additional, Sedlazeck, Fritz, additional, Serrano, Jillian, additional, Shaw, Chad A., additional, Shelford, Tameka, additional, Shively, Kathryn M., additional, Singer-Berk, Moriel, additional, Smith, Joshua D., additional, Snow, Hana, additional, Snyder, Grace, additional, Solomonson, Matthew, additional, Son, Rachel G., additional, Song, Xiaofei, additional, Stankiewicz, Pawel, additional, Stephan, Taylorlyn, additional, Sutton, V. Reid, additional, Sveden, Abigail, additional, Sánchez, Diana Cornejo, additional, Tackett, Monica, additional, Talkowski, Michael, additional, Threlkeld, Machiko S., additional, Tiao, Grace, additional, Udler, Miriam S., additional, Vail, Laura, additional, Valivullah, Zaheer, additional, Valkanas, Elise, additional, VanNoy, Grace E., additional, Wang, Qingbo S., additional, Wang, Gao, additional, Wang, Lu, additional, Wangler, Michael F., additional, Watts, Nicholas A., additional, Weisburd, Ben, additional, Weiss, Jeffrey M., additional, Wheeler, Marsha M., additional, White, Janson J., additional, Williamson, Clara E., additional, Wilson, Michael W., additional, Wiszniewski, Wojciech, additional, Withers, Marjorie A., additional, Witmer, Dane, additional, Witzgall, Lauren, additional, Wohler, Elizabeth, additional, Wojcik, Monica H., additional, Wong, Isaac, additional, Wood, Jordan C., additional, Wu, Nan, additional, Xing, Jinchuan, additional, Yang, Yaping, additional, Yi, Qian, additional, Yuan, Bo, additional, Zeiger, Jordan E., additional, Zhang, Chaofan, additional, Zhang, Peng, additional, Zhang, Yan, additional, Zhang, Xiaohong, additional, Zhang, Yeting, additional, Zhang, Shifa, additional, Zoghbi, Huda, additional, and van den Veyver, Igna, additional

Published
2022
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7. Additional file 2 of Recommendations for clinical interpretation of variants found in non-coding regions of the genome

Author

Ellingford, Jamie M., Ahn, Joo Wook, Bagnall, Richard D., Baralle, Diana, Barton, Stephanie, Campbell, Chris, Downes, Kate, Ellard, Sian, Duff-Farrier, Celia, FitzPatrick, David R., Greally, John M., Ingles, Jodie, Krishnan, Neesha, Lord, Jenny, Martin, Hilary C., Newman, William G., O’Donnell-Luria, Anne, Ramsden, Simon C., Rehm, Heidi L., Richardson, Ebony, Singer-Berk, Moriel, Taylor, Jenny C., Williams, Maggie, Wood, Jordan C., Wright, Caroline F., Harrison, Steven M., and Whiffin, Nicola

Abstract

Additional file 2: Fig S1. Identifying regulatory variants in trans with pLoF variants in GEL.

Published
2022
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8. Recommendations for clinical interpretation of variants found in non-coding regions of the genome

Author

Ellingford, Jamie M, primary, Ahn, Joo Wook, additional, Bagnall, Richard D, additional, Baralle, Diana, additional, Barton, Stephanie, additional, Campbell, Chris, additional, Downes, Kate, additional, Ellard, Sian, additional, Duff-Farrier, Celia, additional, FitzPatrick, David R, additional, Ingles, Jodie, additional, Krishnan, Neesha, additional, Lord, Jenny, additional, Martin, Hilary C, additional, Newman, William G, additional, O’Donnell-Luria, Anne, additional, Ramsden, Simon C, additional, Rehm, Heidi L, additional, Richardson, Ebony, additional, Singer-Berk, Moriel, additional, Taylor, Jenny C, additional, Williams, Maggie, additional, Wood, Jordan C, additional, Wright, Caroline F, additional, Harrison, Steven M, additional, and Whiffin, Nicola, additional

Published
2021
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10. Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy

Author

O'Donnell-Luria, Anne H, Pais, Lynn S, Faundes, Víctor, Wood, Jordan C, Sveden, Abigail, Luria, Victor, Abou Jamra, Rami, Accogli, Andrea, Amburgey, Kimberly, Anderlid, Britt Marie, Azzarello-Burri, Silvia, Basinger, Alice A, Bianchini, Claudia, Bird, Lynne M, Buchert, Rebecca, Carre, Wilfrid, Ceulemans, Sophia, Charles, Perrine, Cox, Helen, Culliton, Lisa, Currò, Aurora, Deciphering Developmental Disorders (DDD) Study, Demurger, Florence, Dowling, James J, Duban-Bedu, Benedicte, Dubourg, Christèle, Eiset, Saga Elise, Escobar, Luis F, Ferrarini, Alessandra, Haack, Tobias B, Hashim, Mona, Heide, Solveig, Helbig, Katherine L, Helbig, Ingo, Heredia, Raul, Héron, Delphine, Isidor, Bertrand, Jonasson, Amy R, Joset, Pascal, Keren, Boris, Kok, Fernando, Kroes, Hester Y, Lavillaureix, Alinoë, Lu, Xin, Maas, Saskia M, Maegawa, Gustavo HB, Marcelis, Carlo LM, Mark, Paul R, Masruha, Marcelo R, McLaughlin, Heather M, McWalter, Kirsty, Melchinger, Esther U, Mercimek-Andrews, Saadet, Nava, Caroline, Pendziwiat, Manuela, Person, Richard, Ramelli, Gian Paolo, Ramos, Luiza LP, Rauch, Anita, Reavey, Caitlin, Renieri, Alessandra, Rieß, Angelika, Sanchez-Valle, Amarilis, Sattar, Shifteh, Saunders, Carol, Schwarz, Niklas, Smol, Thomas, Srour, Myriam, Steindl, Katharina, Syrbe, Steffen, Taylor, Jenny C, Telegrafi, Aida, Thiffault, Isabelle, Trauner, Doris A, van der Linden, Helio, van Koningsbruggen, Silvana, Villard, Laurent, Vogel, Ida, Vogt, Julie, Weber, Yvonne G, Wentzensen, Ingrid M, Widjaja, Elysa, Zak, Jaroslav, Baxter, Samantha, Banka, Siddharth, and Rodan, Lance H

Subjects
Adult, Male, Heterozygote, Adolescent, Intellectual and Developmental Disabilities (IDD), Autism, global developmental delay, Haploinsufficiency, Neurodegenerative, H3K4 methylation, Medical and Health Sciences, Young Adult, Clinical Research, Deciphering Developmental Disorders (DDD) Study, Humans, 2.1 Biological and endogenous factors, Aetiology, Child, Preschool, Pediatric, Genetics & Heredity, Epilepsy, Neurosciences, Infant, Genetic Variation, Biological Sciences, neurodevelopmental disorder, Pedigree, KMT2E, Brain Disorders, DNA-Binding Proteins, Phenotype, epileptic encephalopathy, Mental Health, Neurodevelopmental Disorders, intellectual disability, Neurological, Female
Abstract

We delineate a KMT2E-related neurodevelopmental disorder on the basis of 38 individuals in 36 families. This study includes 31 distinct heterozygous variants in KMT2E (28 ascertained from Matchmaker Exchange and three previously reported), and four individuals with chromosome 7q22.2-22.23 microdeletions encompassing KMT2E (one previously reported). Almost all variants occurred de novo, and most were truncating. Most affected individuals with protein-truncating variants presented with mild intellectual disability. One-quarter of individuals met criteria for autism. Additional common features include macrocephaly, hypotonia, functional gastrointestinal abnormalities, and a subtle facial gestalt. Epilepsy was present in about one-fifth of individuals with truncating variants and was responsive to treatment with anti-epileptic medications in almost all. More than 70% of the individuals were male, and expressivity was variable by sex; epilepsy was more common in females and autism more common in males. The four individuals with microdeletions encompassing KMT2E generally presented similarly to those with truncating variants, but the degree of developmental delay was greater. The group of four individuals with missense variants in KMT2E presented with the most severe developmental delays. Epilepsy was present in all individuals with missense variants, often manifesting as treatment-resistant infantile epileptic encephalopathy. Microcephaly was also common in this group. Haploinsufficiency versus gain-of-function or dominant-negative effects specific to these missense variants in KMT2E might explain this divergence in phenotype, but requires independent validation. Disruptive variants in KMT2E are an under-recognized cause of neurodevelopmental abnormalities.

Published
2019

12. Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy.

Author

O'Donnell-Luria, Anne H., Pais, Lynn S., Faundes, Víctor, Wood, Jordan C., Sveden, Abigail, Luria, Victor, Abou Jamra, Rami, Accogli, Andrea, Amburgey, Kimberly, Anderlid, Britt Marie, Azzarello-Burri, Silvia, Basinger, Alice A., Bianchini, Claudia, Bird, Lynne M., Buchert, Rebecca, Carre, Wilfrid, Ceulemans, Sophia, Charles, Perrine, Cox, Helen, and Culliton, Lisa

Subjects
*EPILEPSY, *DISABILITIES, *DEVELOPMENTAL delay, *INTELLECTUAL disabilities, *DISEASES
Abstract

We delineate a KMT2E -related neurodevelopmental disorder on the basis of 38 individuals in 36 families. This study includes 31 distinct heterozygous variants in KMT2E (28 ascertained from Matchmaker Exchange and three previously reported), and four individuals with chromosome 7q22.2-22.23 microdeletions encompassing KMT2E (one previously reported). Almost all variants occurred de novo , and most were truncating. Most affected individuals with protein-truncating variants presented with mild intellectual disability. One-quarter of individuals met criteria for autism. Additional common features include macrocephaly, hypotonia, functional gastrointestinal abnormalities, and a subtle facial gestalt. Epilepsy was present in about one-fifth of individuals with truncating variants and was responsive to treatment with anti-epileptic medications in almost all. More than 70% of the individuals were male, and expressivity was variable by sex; epilepsy was more common in females and autism more common in males. The four individuals with microdeletions encompassing KMT2E generally presented similarly to those with truncating variants, but the degree of developmental delay was greater. The group of four individuals with missense variants in KMT2E presented with the most severe developmental delays. Epilepsy was present in all individuals with missense variants, often manifesting as treatment-resistant infantile epileptic encephalopathy. Microcephaly was also common in this group. Haploinsufficiency versus gain-of-function or dominant-negative effects specific to these missense variants in KMT2E might explain this divergence in phenotype, but requires independent validation. Disruptive variants in KMT2E are an under-recognized cause of neurodevelopmental abnormalities. [ABSTRACT FROM AUTHOR]

Published
2019
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13. Adherence to adult clinical practice guidelines for Down syndrome.

Author

Wood JC, Gochyyev P, and Santoro SL

Abstract

Adults with Down syndrome (DS) have unique health care needs with evidence-based care guidelines to address these. Yet, the 2020 adult guidelines were unstudied; we aimed to assess adherence to these guidelines. We reviewed clinical and demographic data from medical charts of 327 adults with DS who were seen in the MGH DSP. We calculated adherence to care guidelines and analyzed correlations between both demographic traits and clinical results. Mean adherence rate to each of the nine adult guidelines was 67.3%. Adherence rates that were below our mean adherence rate included colonoscopy (42.9%), iron (41.9%), audiology specialist (35.8%), and audiogram (35.2%). We found four significant correlations: assigned females at birth had a significantly higher body mass index (BMI) than assigned males at birth (p < 0.001), Hispanic patients had a significantly higher BMI than other patients (p = 0.015), Hispanic patients had a significantly higher rate of diabetes than other patients (p = 0.036), and Black patients had a significantly lower rate of hypothyroidism than other patients (p = 0.004). We assessed the adherence rates to adult DS guidelines and highlighted disparities in healthcare for patients with DS to inform clinicians on how to improve care for patients with DS., (© 2024 Wiley Periodicals LLC.)

Published
2024
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14. Advanced variant classification framework reduces the false positive rate of predicted loss of function (pLoF) variants in population sequencing data.

Author

Singer-Berk M, Gudmundsson S, Baxter S, Seaby EG, England E, Wood JC, Son RG, Watts NA, Karczewski KJ, Harrison SM, MacArthur DG, Rehm HL, and O'Donnell-Luria A

Abstract

Predicted loss of function (pLoF) variants are highly deleterious and play an important role in disease biology, but many of these variants may not actually result in loss-of-function. Here we present a framework that advances interpretation of pLoF variants in research and clinical settings by considering three categories of LoF evasion: (1) predicted rescue by secondary sequence properties, (2) uncertain biological relevance, and (3) potential technical artifacts. We also provide recommendations on adjustments to ACMG/AMP guidelines's PVS1 criterion. Applying this framework to all high-confidence pLoF variants in 22 autosomal recessive disease-genes from the Genome Aggregation Database (gnomAD, v2.1.1) revealed predicted LoF evasion or potential artifacts in 27.3% (304/1,113) of variants. The major reasons were location in the last exon, in a homopolymer repeat, in low per-base expression (pext) score regions, or the presence of cryptic splice rescues. Variants predicted to be potential artifacts or to evade LoF were enriched for ClinVar benign variants. PVS1 was downgraded in 99.4% (162/163) of LoF evading variants assessed, with 17.2% (28/163) downgraded as a result of our framework, adding to previous guidelines. Variant pathogenicity was affected (mostly from likely pathogenic to VUS) in 20 (71.4%) of these 28 variants. This framework guides assessment of pLoF variants beyond standard annotation pipelines, and substantially reduces false positive rates, which is key to ensure accurate LoF variant prediction in both a research and clinical setting.

Published
2023
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