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116 results on '"Du, Haowei"'

1. Evidence-Enhanced Triplet Generation Framework for Hallucination Alleviation in Generative Question Answering

Author

Du, Haowei, Zhang, Huishuai, and Zhao, Dongyan

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence
Abstract

To address the hallucination in generative question answering (GQA) where the answer can not be derived from the document, we propose a novel evidence-enhanced triplet generation framework, EATQA, encouraging the model to predict all the combinations of (Question, Evidence, Answer) triplet by flipping the source pair and the target label to understand their logical relationships, i.e., predict Answer(A), Question(Q), and Evidence(E) given a QE, EA, and QA pairs, respectively. Furthermore, we bridge the distribution gap to distill the knowledge from evidence in inference stage. Our framework ensures the model to learn the logical relation between query, evidence and answer, which simultaneously improves the evidence generation and query answering. In this paper, we apply EATQA to LLama and it outperforms other LLMs-based methods and hallucination mitigation approaches on two challenging GQA benchmarks. Further analysis shows that our method not only keeps prior knowledge within LLM, but also mitigates hallucination and generates faithful answers.

Published
2024

2. In-Context Learning with Reinforcement Learning for Incomplete Utterance Rewriting

Author

Du, Haowei and Zhao, Dongyan

Subjects
Computer Science - Computation and Language
Abstract

In-context learning (ICL) of large language models (LLMs) has attracted increasing attention in the community where LLMs make predictions only based on instructions augmented with a few examples. Existing example selection methods for ICL utilize sparse or dense retrievers and derive effective performance. However, these methods do not utilize direct feedback of LLM to train the retriever and the examples selected can not necessarily improve the analogy ability of LLM. To tackle this, we propose our policy-based reinforcement learning framework for example selection (RLS), which consists of a language model (LM) selector and an LLM generator. The LM selector encodes the candidate examples into dense representations and selects the top-k examples into the demonstration for LLM. The outputs of LLM are adopted to compute the reward and policy gradient to optimize the LM selector. We conduct experiments on different datasets and significantly outperform existing example selection methods. Moreover, our approach shows advantages over supervised finetuning (SFT) models in few shot setting. Further experiments show the balance of abundance and the similarity with the test case of examples is important for ICL performance of LLM.

Published
2024

3. Internal and External Knowledge Interactive Refinement Framework for Knowledge-Intensive Question Answering

Author

Du, Haowei and Zhao, Dongyan

Subjects
Computer Science - Computation and Language
Abstract

Recent works have attempted to integrate external knowledge into LLMs to address the limitations and potential factual errors in LLM-generated content. However, how to retrieve the correct knowledge from the large amount of external knowledge imposes a challenge. To this end, we empirically observe that LLMs have already encoded rich knowledge in their pretrained parameters and utilizing these internal knowledge improves the retrieval of external knowledge when applying them to knowledge-intensive tasks. In this paper, we propose a new internal and external knowledge interactive refinement paradigm dubbed IEKR to utilize internal knowledge in LLM to help retrieve relevant knowledge from the external knowledge base, as well as exploit the external knowledge to refine the hallucination of generated internal knowledge. By simply adding a prompt like 'Tell me something about' to the LLMs, we try to review related explicit knowledge and insert them with the query into the retriever for external retrieval. The external knowledge is utilized to complement the internal knowledge into input of LLM for answers. We conduct experiments on 3 benchmark datasets in knowledge-intensive question answering task with different LLMs and domains, achieving the new state-of-the-art. Further analysis shows the effectiveness of different modules in our approach.

Published
2024

4. Multi-Granularity Information Interaction Framework for Incomplete Utterance Rewriting

Author

Du, Haowei, Zhang, Dinghao, Li, Chen, Li, Yang, and Zhao, Dongyan

Subjects
Computer Science - Computation and Language
Abstract

Recent approaches in Incomplete Utterance Rewriting (IUR) fail to capture the source of important words, which is crucial to edit the incomplete utterance, and introduce words from irrelevant utterances. We propose a novel and effective multi-task information interaction framework including context selection, edit matrix construction, and relevance merging to capture the multi-granularity of semantic information. Benefiting from fetching the relevant utterance and figuring out the important words, our approach outperforms existing state-of-the-art models on two benchmark datasets Restoration-200K and CANAND in this field. Code will be provided on \url{https://github.com/yanmenxue/QR}., Comment: Findings of EMNLP2023 (short)

Published
2023

5. Relation-Aware Question Answering for Heterogeneous Knowledge Graphs

Author

Du, Haowei, Huang, Quzhe, Li, Chen, Zhang, Chen, Li, Yang, and Zhao, Dongyan

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence
Abstract

Multi-hop Knowledge Base Question Answering(KBQA) aims to find the answer entity in a knowledge graph (KG), which requires multiple steps of reasoning. Existing retrieval-based approaches solve this task by concentrating on the specific relation at different hops and predicting the intermediate entity within the reasoning path. During the reasoning process of these methods, the representation of relations are fixed but the initial relation representation may not be optimal. We claim they fail to utilize information from head-tail entities and the semantic connection between relations to enhance the current relation representation, which undermines the ability to capture information of relations in KGs. To address this issue, we construct a \textbf{dual relation graph} where each node denotes a relation in the original KG (\textbf{primal entity graph}) and edges are constructed between relations sharing same head or tail entities. Then we iteratively do primal entity graph reasoning, dual relation graph information propagation, and interaction between these two graphs. In this way, the interaction between entity and relation is enhanced, and we derive better entity and relation representations. Experiments on two public datasets, WebQSP and CWQ, show that our approach achieves a significant performance gain over the prior state-of-the-art. Our code is available on \url{https://github.com/yanmenxue/RAH-KBQA}., Comment: Findings of EMNLP2023 (Long)

Published
2023

6. Investigation of Smart Nano Rotor with Continuous Trailing Edge Flap Driven by Electroactive Polymer

Author

Kang, Zihan, Liu, Zhen, Zhao, Fengwan, Zhang, Jie, Du, Haowei, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Tan, Kay Chen, Series Editor, and Fu, Song, editor

Published
2024
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7. Cross-Lingual Question Answering over Knowledge Base as Reading Comprehension

Author

Zhang, Chen, Lai, Yuxuan, Feng, Yansong, Shen, Xingyu, Du, Haowei, and Zhao, Dongyan

Subjects
Computer Science - Computation and Language
Abstract

Although many large-scale knowledge bases (KBs) claim to contain multilingual information, their support for many non-English languages is often incomplete. This incompleteness gives birth to the task of cross-lingual question answering over knowledge base (xKBQA), which aims to answer questions in languages different from that of the provided KB. One of the major challenges facing xKBQA is the high cost of data annotation, leading to limited resources available for further exploration. Another challenge is mapping KB schemas and natural language expressions in the questions under cross-lingual settings. In this paper, we propose a novel approach for xKBQA in a reading comprehension paradigm. We convert KB subgraphs into passages to narrow the gap between KB schemas and questions, which enables our model to benefit from recent advances in multilingual pre-trained language models (MPLMs) and cross-lingual machine reading comprehension (xMRC). Specifically, we use MPLMs, with considerable knowledge of cross-lingual mappings, for cross-lingual reading comprehension. Existing high-quality xMRC datasets can be further utilized to finetune our model, greatly alleviating the data scarcity issue in xKBQA. Extensive experiments on two xKBQA datasets in 12 languages show that our approach outperforms various baselines and achieves strong few-shot and zero-shot performance. Our dataset and code are released for further research., Comment: 14 pages, 4 figures, EACL 2023 (findings)

Published
2023

8. Knowledge-enhanced Iterative Instruction Generation and Reasoning for Knowledge Base Question Answering

Author

Du, Haowei, Huang, Quzhe, Zhang, Chen, and Zhao, Dongyan

Subjects
Computer Science - Computation and Language
Abstract

Multi-hop Knowledge Base Question Answering(KBQA) aims to find the answer entity in a knowledge base which is several hops from the topic entity mentioned in the question. Existing Retrieval-based approaches first generate instructions from the question and then use them to guide the multi-hop reasoning on the knowledge graph. As the instructions are fixed during the whole reasoning procedure and the knowledge graph is not considered in instruction generation, the model cannot revise its mistake once it predicts an intermediate entity incorrectly. To handle this, we propose KBIGER(Knowledge Base Iterative Instruction GEnerating and Reasoning), a novel and efficient approach to generate the instructions dynamically with the help of reasoning graph. Instead of generating all the instructions before reasoning, we take the (k-1)-th reasoning graph into consideration to build the k-th instruction. In this way, the model could check the prediction from the graph and generate new instructions to revise the incorrect prediction of intermediate entities. We do experiments on two multi-hop KBQA benchmarks and outperform the existing approaches, becoming the new-state-of-the-art. Further experiments show our method does detect the incorrect prediction of intermediate entities and has the ability to revise such errors., Comment: Accepted by NLPCC 2022(oral)

Published
2022

9. Phenotypic and mutational spectrum of ROR2‐related Robinow syndrome

Author

Lima, Ariadne R, Ferreira, Barbara M, Zhang, Chaofan, Jolly, Angad, Du, Haowei, White, Janson J, Dawood, Moez, Lins, Tulio C, Chiabai, Marcela A, Beusekom, Ellen, Cordoba, Mara S, Rosa, Erica CC Caldas, Kayserili, Hulya, Kimonis, Virginia, Wu, Erica, Mellado, Cecilia, Aggarwal, Vineet, Richieri‐Costa, Antonio, Brunoni, Décio, Canó, Talyta M, Jorge, Alexander AL, Kim, Chong A, Honjo, Rachel, Bertola, Débora R, Dandalo‐Girardi, Raissa M, Bayram, Yavuz, Gezdirici, Alper, Yilmaz‐Gulec, Elif, Gumus, Evren, Yilmaz, Gülay C, Okamoto, Nobuhiko, Ohashi, Hirofumi, Coban–Akdemir, Zeynep, Mitani, Tadahiro, Jhangiani, Shalini N, Muzny, Donna M, Regattieri, Neysa AP, Pogue, Robert, Pereira, Rinaldo W, Otto, Paulo A, Gibbs, Richard A, Ali, Bassam R, Bokhoven, Hans, Brunner, Han G, Sutton, V Reid, Lupski, James R, Vianna‐Morgante, Angela M, Carvalho, Claudia MB, and Mazzeu, Juliana F

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Clinical Research, Pediatric, Congenital Structural Anomalies, Aetiology, 2.1 Biological and endogenous factors, Craniofacial Abnormalities, Dwarfism, Genes, Recessive, Humans, Limb Deformities, Congenital, Male, Phenotype, Receptor Tyrosine Kinase-like Orphan Receptors, Urogenital Abnormalities, chromosome microarray analysis, craniofacial morphology, exonic deletion, HPO terms, next-generation sequencing, quantitative phenotyping cluster heatmap, skeletal dysplasia, WNT pathway, Clinical Sciences, Genetics & Heredity, Clinical sciences
Abstract

Robinow syndrome is characterized by a triad of craniofacial dysmorphisms, disproportionate-limb short stature, and genital hypoplasia. A significant degree of phenotypic variability seems to correlate with different genes/loci. Disturbances of the noncanonical WNT-pathway have been identified as the main cause of the syndrome. Biallelic variants in ROR2 cause an autosomal recessive form of the syndrome with distinctive skeletal findings. Twenty-two patients with a clinical diagnosis of autosomal recessive Robinow syndrome were screened for variants in ROR2 using multiple molecular approaches. We identified 25 putatively pathogenic ROR2 variants, 16 novel, including single nucleotide variants and exonic deletions. Detailed phenotypic analyses revealed that all subjects presented with a prominent forehead, hypertelorism, short nose, abnormality of the nasal tip, brachydactyly, mesomelic limb shortening, short stature, and genital hypoplasia in male patients. A total of 19 clinical features were present in more than 75% of the subjects, thus pointing to an overall uniformity of the phenotype. Disease-causing variants in ROR2, contribute to a clinically recognizable autosomal recessive trait phenotype with multiple skeletal defects. A comprehensive quantitative clinical evaluation of this cohort delineated the phenotypic spectrum of ROR2-related Robinow syndrome. The identification of exonic deletion variant alleles further supports the contention of a loss-of-function mechanism in the etiology of the syndrome.

Published
2022

10. Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci

Author

Grochowski, Christopher M., Bengtsson, Jesse D., Du, Haowei, Gandhi, Mira, Lun, Ming Yin, Mehaffey, Michele G., Park, KyungHee, Höps, Wolfram, Benito, Eva, Hasenfeld, Patrick, Korbel, Jan O., Mahmoud, Medhat, Paulin, Luis F., Jhangiani, Shalini N., Hwang, James Paul, Bhamidipati, Sravya V., Muzny, Donna M., Fatih, Jawid M., Gibbs, Richard A., Pendleton, Matthew, Harrington, Eoghan, Juul, Sissel, Lindstrand, Anna, Sedlazeck, Fritz J., Pehlivan, Davut, Lupski, James R., and Carvalho, Claudia M.B.

Published
2024
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13. Haploinsufficiency of ZFHX3, encoding a key player in neuronal development, causes syndromic intellectual disability

Author

Agrawal, Pankaj, Armstrong Scott, Daryl, Barkoudah, Elizabeth, Bellini, Melissa, Beneteau, Claire, Bjørgo, Kathrine, Brooks, Alice, Brown, Natasha, Castle, Alison, Castro, Diana, Chorin, Odelia, Cleghorn, Mark, Clement, Emma, Coman, David, Costin, Carrie, Devriendt, Koen, Dong, Dexin, Dries, Annika, Duelund Hjortshøj, Tina, Dyment, David, Eng, Christine, Genetti, Casie, Grano, Siera, Henneman, Peter, Heron, Delphine, Hoffmann, Katrin, Hom, Jason, Du, Haowei, Iascone, Maria, Isidor, Bertrand, Järvelä, Irma E., Jones, Julie, Keren, Boris, Koenig, Mary Kay, Kohlhase, Jürgen, Lalani, Seema, Le Caignec, Cedric, Lewis, Andi, Liu, Pengfei, Lovgren, Alysia, Lupski, James R., Lyons, Mike, Lysy, Philippe, Manning, Melanie, Marcelis, Carlo, McLean, Scott Douglas, Mercie, Sandra, Mertens, Mareike, Molin, Arnaud, Nizon, Mathilde, Nugent, Kimberly Margaret, Öhman, Susanna, O'Leary, Melanie, Okashah Littlejohn, Rebecca, Petit, Florence, Pfundt, Rolph, Pottocki, Lorraine, Raas-Rotschild, Annick, Ranguin, Kara, Revencu, Nicole, Rosenfeld, Jill, Rhodes, Lindsay, Santos Simmaro, Fernando, Sals, Karen, Schieving, Jolanda, Schrauwen, Isabelle, Schuurs-Hoeijmakers, Janneke H.M., Seaby, Eleanor G., Sheffer, Ruth, Snijders Blok, Lot, Sørensen, Kristina P., Srivastava, Siddharth, Stark, Zornitza, Stoeva, Radka, Stutterd, Chloe, Tan, Natalie B., Mathiesen Torring, Pernille, Vanakker, Olivier, van der Laan, Liselot, Ververi, Athina, Villavicencio-Lorini, Pablo, Vincent, Marie, Wand, Dorothea, Wessels, Marja, White, Sue, Wojcik, Monica H., Wu, Nan, Zhao, Sen, Pérez Baca, María del Rocío, Jacobs, Eva Z., Vantomme, Lies, Leblanc, Pontus, Bogaert, Elke, Dheedene, Annelies, De Cock, Laurenz, Haghshenas, Sadegheh, Foroutan, Aidin, Levy, Michael A., Kerkhof, Jennifer, McConkey, Haley, Chen, Chun-An, Batzir, Nurit Assia, Wang, Xia, Palomares, María, Carels, Marieke, Dermaut, Bart, Sadikovic, Bekim, Menten, Björn, Yuan, Bo, Vergult, Sarah, and Callewaert, Bert

Published
2024
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14. Beyond the exome: What’s next in diagnostic testing for Mendelian conditions

Author

Abouhala, Siwaar, Albert, Jessica, Almalvez, Miguel, Alvarez, Raquel, Amin, Mutaz, Anderson, Peter, Aradhya, Swaroop, Ashley, Euan, Assimes, Themistocles, Auriga, Light, Austin-Tse, Christina, Bamshad, Mike, Barseghyan, Hayk, Baxter, Samantha, Behera, Sairam, Beheshti, Shaghayegh, Bejerano, Gill, Berger, Seth, Bernstein, Jon, Best, Sabrina, Blankenmeister, Benjamin, Blue, Elizabeth, Boerwinkle, Eric, Bonkowski, Emily, Bonner, Devon, Boone, Philip, Bornhorst, Miriam, Bozkurt-Yozgatli, Tugce, Brand, Harrison, Buckingham, Kati, Calame, Daniel, Casadei, Silvia, Chadwick, Lisa, Chavez, Clarisa, Chen, Ziwei, Chinn, Ivan, Chong, Jessica, Coban-Akdemir, Zeynep, Cohen, Andrea J., Conner, Sarah, Conomos, Matthew, Coveler, Karen, Cui, Ya Allen, Currin, Sara, Daber, Robert, Dardas, Zain, Davis, Colleen, Dawood, Moez, de Dios, Ivan, de Esch, Celine, Delaney, Meghan, Délot, Emmanuèle, DiTroia, Stephanie, Doddapaneni, Harsha, Du, Haowei, Duan, Ruizhi, Dugan-Perez, Shannon, Duong, Nhat, Duyzend, Michael, Eichler, Evan, Emami, Sara, Fatih, Jawid, Fraser, Jamie, Fusaro, Vincent, Galey, Miranda, Ganesh, Vijay, Garimella, Kiran, Gibbs, Richard, Gifford, Casey, Ginsburg, Amy, Goddard, Pagé, Gogarten, Stephanie, Gogate, Nikhita, Gordon, William, Gorzynski, John E., Greenleaf, William, Grochowski, Christopher, Groopman, Emily, Guarischi Sousa, Rodrigo, Gudmundsson, Sanna, Gulati, Ashima, Guo, Daniel, Hale, Walker, Hall, Stacey, Harvey, William, Hawley, Megan, Heavner, Ben, Herman, Isabella, Horike-Pyne, Martha, Hu, Jianhong, Huang, Yongqing, Hwang, James, Jarvik, Gail, Jensen, Tanner, Jhangiani, Shalini, Jimenez-Morales, David, Jin, Christopher, Saad, Ahmed K., Kahn-Kirby, Amanda, Kain, Jessica, Kaur, Parneet, Keehan, Laura, Knoblach, Susan, Ko, Arthur, Kohler, Jennefer, Kundaje, Anshul, Kundu, Soumya, Lancaster, Samuel M., Larsson, Katie, Lemire, Gabrielle, Lewis, Richard, Li, Wei, Li, Yidan, Liu, Pengfei, LoTempio, Jonathan, Lupski, James, Ma, Jialan, MacArthur, Daniel, Mahmoud, Medhat, Malani, Nirav, Mangilog, Brian, Marafi, Dana, Marmolejos, Sofia, Marten, Daniel, Martinez, Eva, Marvin, Colby, Marwaha, Shruti, Kumara Mastrorosa, Francesco, Matalon, Dena, May, Susanne, McGee, Sean, Meador, Lauren, Mefford, Heather, Rodrigo Mendez, Hector, Miller, Alexander, Miller, Danny E., Mitani, Tadahiro, Montgomery, Stephen, Moussa, Hala Mohamed, Moyses, Mariana, Munderloh, Chloe, Muzny, Donna, Nelson, Sarah, Neu, Matthew B., Nguyen, Jonathan, Nguyen, Thuy-mi P., Nussbaum, Robert, Nykamp, Keith, O'Callaghan, William, O'Heir, Emily, O'Leary, Melanie, Olsen, Jeren, Osei-Owusu, Ikeoluwa, O'Donnell-Luria, Anne, Padhi, Evin, Pais, Lynn, Pan, Miao, Panchal, Piyush, Patterson, Karynne, Payne, Sheryl, Pehlivan, Davut, Petrowski, Paul, Pham, Alicia, Pitsava, Georgia, Podesta, Astaria, Ponce, Sarah, Posey, Jennifer, Prosser, Jaime, Quertermous, Thomas, Rai, Archana, Ramani, Arun, Rehm, Heidi, Reuter, Chloe, Reuter, Jason, Richardson, Matthew, Rivera-Munoz, Andres, Rubio, Oriane, Sabo, Aniko, Salani, Monica, Samocha, Kaitlin, Sanchis-Juan, Alba, Savage, Sarah, Scott, Stuart, Scott, Evette, Sedlazeck, Fritz, Shah, Gulalai, Shojaie, Ali, Singh, Mugdha, Smith, Josh, Smith, Kevin, Snow, Hana, Snyder, Michael, Socarras, Kayla, Starita, Lea, Stark, Brigitte, Stenton, Sarah, Stergachis, Andrew, Stilp, Adrienne, Sundaram, Laksshman, Sutton, V. Reid, Tai, Jui-Cheng, Talkowski, Michael, Tise, Christina, Tong, Catherine, Tsao, Philip, Ungar, Rachel, VanNoy, Grace, Vilain, Eric, Voutos, Isabella, Walker, Kim, Weisburd, Ben, Weiss, Jeff, Wellington, Chris, Weng, Ziming, Westheimer, Emily, Wheeler, Marsha, Wheeler, Matthew, Wiel, Laurens, Wilson, Michael, Wojcik, Monica, Wong, Quenna, Wong, Issac, Xiao, Changrui, Yadav, Rachita, Yi, Qian, Yuan, Bo, Zhao, Jianhua, Zhen, Jimmy, Zhou, Harry, Wojcik, Monica H., Reuter, Chloe M., Duyzend, Michael H., Boone, Philip M., Groopman, Emily E., Délot, Emmanuèle C., Jain, Deepti, Starita, Lea M., Montgomery, Stephen B., Bamshad, Michael J., Chong, Jessica X., Wheeler, Matthew T., Berger, Seth I., and Sedlazeck, Fritz J.

Published
2023
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15. Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease

Author

Calame, Daniel G., Guo, Tianyu, Wang, Chen, Garrett, Lillian, Jolly, Angad, Dawood, Moez, Kurolap, Alina, Henig, Noa Zunz, Fatih, Jawid M., Herman, Isabella, Du, Haowei, Mitani, Tadahiro, Becker, Lore, Rathkolb, Birgit, Gerlini, Raffaele, Seisenberger, Claudia, Marschall, Susan, Hunter, Jill V., Gerard, Amanda, Heidlebaugh, Alexis, Challman, Thomas, Spillmann, Rebecca C., Jhangiani, Shalini N., Coban-Akdemir, Zeynep, Lalani, Seema, Liu, Lingxiao, Revah-Politi, Anya, Iglesias, Alejandro, Guzman, Edwin, Baugh, Evan, Boddaert, Nathalie, Rondeau, Sophie, Ormieres, Clothide, Barcia, Giulia, Tan, Queenie K.G., Thiffault, Isabelle, Pastinen, Tomi, Sheikh, Kazim, Biliciler, Suur, Mei, Davide, Melani, Federico, Shashi, Vandana, Yaron, Yuval, Steele, Mary, Wakeling, Emma, Østergaard, Elsebet, Nazaryan-Petersen, Lusine, Millan, Francisca, Santiago-Sim, Teresa, Thevenon, Julien, Bruel, Ange-Line, Thauvin-Robinet, Christel, Popp, Denny, Platzer, Konrad, Gawlinski, Pawel, Wiszniewski, Wojciech, Marafi, Dana, Pehlivan, Davut, Posey, Jennifer E., Gibbs, Richard A., Gailus-Durner, Valerie, Guerrini, Renzo, Fuchs, Helmut, Hrabě de Angelis, Martin, Hölter, Sabine M., Cheung, Hoi-Hung, Gu, Shen, and Lupski, James R.

Published
2023
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16. Rare variant enrichment analysis supports GREB1L as a contributory driver gene in the etiology of Mayer-Rokitansky-Küster-Hauser syndrome

Author

Jolly, Angad, Du, Haowei, Borel, Christelle, Chen, Na, Zhao, Sen, Grochowski, Christopher M., Duan, Ruizhi, Fatih, Jawid M., Dawood, Moez, Salvi, Sejal, Jhangiani, Shalini N., Muzny, Donna M., Koch, André, Rouskas, Konstantinos, Glentis, Stavros, Deligeoroglou, Efthymios, Bacopoulou, Flora, Wise, Carol A., Dietrich, Jennifer E., Van den Veyver, Ignatia B., Dimas, Antigone S., Brucker, Sara, Sutton, V. Reid, Gibbs, Richard A., Antonarakis, Stylianos E., Wu, Nan, Coban-Akdemir, Zeynep H., Zhu, Lan, Posey, Jennifer E., and Lupski, James R.

Published
2023
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18. NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy

Author

Dardas, Zain, primary, Fatih, Jawid M., additional, Jolly, Angad, additional, Dawood, Moez, additional, Du, Haowei, additional, Grochowski, Christopher M., additional, Jones, Edward G., additional, Jhangiani, Shalini N., additional, Wehrens, Xander H. T., additional, Liu, Pengfei, additional, Bi, Weimin, additional, Boerwinkle, Eric, additional, Posey, Jennifer E., additional, Muzny, Donna M., additional, Gibbs, Richard A., additional, Lupski, James R., additional, Coban-Akdemir, Zeynep, additional, and Morris, Shaine A., additional

Published
2024
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19. The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation

Author

Du, Haowei, Jolly, Angad, Grochowski, Christopher M., Yuan, Bo, Dawood, Moez, Jhangiani, Shalini N., Li, He, Muzny, Donna, Fatih, Jawid M., Coban-Akdemir, Zeynep, Carlin, Mary Esther, Scheuerle, Angela E., Witzl, Karin, Posey, Jennifer E., Pendleton, Matthew, Harrington, Eoghan, Juul, Sissel, Hastings, P. J., Bi, Weimin, Gibbs, Richard A., Sedlazeck, Fritz J., Lupski, James R., Carvalho, Claudia M. B., and Liu, Pengfei

Published
2022
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20. Biallelic loss-of-function variants in the splicing regulator NSRP1 cause a severe neurodevelopmental disorder with spastic cerebral palsy and epilepsy

Author

Calame, Daniel G., Bakhtiari, Somayeh, Logan, Rachel, Coban-Akdemir, Zeynep, Du, Haowei, Mitani, Tadahiro, Fatih, Jawid M., Hunter, Jill V., Herman, Isabella, Pehlivan, Davut, Jhangiani, Shalini N., Person, Richard, Schnur, Rhonda E., Jin, Sheng Chih, Bilguvar, Kaya, Posey, Jennifer E., Koh, Sookyong, Firouzabadi, Saghar G., Alehabib, Elham, Tafakhori, Abbas, Esmkhani, Sahra, Gibbs, Richard A., Noureldeen, Mahmoud M., Zaki, Maha S., Marafi, Dana, Darvish, Hossein, Kruer, Michael C., and Lupski, James R.

Published
2021
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22. Genomic Balancing Act: Deciphering DNA rearrangements in the Complex Chromosomal Aberration involving 5p15.2, 2q31.1 and 18q21.32

Author

Lupski, James, primary, Dardas, Zain, additional, Marafi, Dana, additional, Duan, Ruizhi, additional, Fatih, Jawid, additional, El-Rashidy, Omnia, additional, Grochowski, Christopher, additional, Carvalho, Claudia, additional, Jhangiani, Shalini, additional, Bi, Weimin, additional, Du, Haowei, additional, Gibbs, Richard, additional, Posey, Jennifer, additional, Calame, Daniel, additional, and Zaki, Maha, additional

Published
2024
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23. Biallelic variation in the choline and ethanolamine transporter FLVCR1 underlies a pleiotropic disease spectrum from adult neurodegeneration to severe developmental disorders

Author

Calame, Daniel G, primary, Wong, Jovi Huixin, additional, Panda, Puravi, additional, Nguyen, Dat Tuan, additional, Leong, Nancy C.P., additional, Sangermano, Riccardo, additional, Patankar, Sohil G, additional, AlAbdi, Lama, additional, Safwat, Sylvia, additional, Flannery, Kyle, additional, Dardas, Zain, additional, Fatih, Jawid M, additional, Murali, Chaya, additional, Kannan, Varun, additional, Lotze, Timothy E, additional, Herman, Isabella, additional, Ammouri, Farrah, additional, Rezich, Brianna, additional, Efthymiou, Stephanie, additional, Alavi, Shahryar, additional, Murphy, David, additional, Firoozfar, Zahra, additional, Nasab, Mahya Ebrahimi, additional, Bahreini, Amir, additional, Ghasemi, Majid, additional, Haridy, Nourelhoda A, additional, Goldouzi, Hamid Reza, additional, Eghbal, Fatemeh, additional, Karimiani, Ehsan Ghayoor, additional, Srinivasan, Varunvenkat M, additional, Gowda, Vykuntaraju K, additional, Du, Haowei, additional, Jhangiani, Shalini N, additional, Coban-Akdemir, Zeynep, additional, Marafi, Dana, additional, Rodan, Lance, additional, Isikay, Sedat, additional, Rosenfeld, Jill A, additional, Ramanathan, Subhadra, additional, Staton, Michael, additional, Oberg, Kerby C, additional, Clark, Robin D, additional, Wenman, Catharina, additional, Loughlin, Sam, additional, Saad, Ramy, additional, Ashraf, Tazeen, additional, Male, Alison, additional, Tadros, Shereen, additional, Boostani, Reza, additional, Abdel-Salam, Ghada H.M., additional, Zaki, Maha, additional, Abdalla, Ebtesam, additional, Manzini, M Chiara, additional, Pehlivan, Davut, additional, Posey, Jennifer E, additional, Gibbs, Richard A, additional, Houlden, Henry, additional, Alkuraya, Fowzan S, additional, Bujakowska, Kinga, additional, Maroofian, Reza, additional, Lupski, James R, additional, and Nguyen, Long Nam, additional

Published
2024
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25. HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data

Author

Du, Haowei, primary, Dardas, Zain, additional, Jolly, Angad, additional, Grochowski, Christopher M, additional, Jhangiani, Shalini N, additional, Li, He, additional, Muzny, Donna, additional, Fatih, Jawid M, additional, Yesil, Gozde, additional, Elçioglu, Nursel H, additional, Gezdirici, Alper, additional, Marafi, Dana, additional, Pehlivan, Davut, additional, Calame, Daniel G, additional, Carvalho, Claudia M B, additional, Posey, Jennifer E, additional, Gambin, Tomasz, additional, Coban-Akdemir, Zeynep, additional, and Lupski, James R, additional

Published
2023
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26. Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures

Author

Grochowski, Christopher M., primary, Bengtsson, Jesse D., additional, Du, Haowei, additional, Gandhi, Mira, additional, Lun, Ming Yin, additional, Mehaffey, Michele G., additional, Park, KyungHee, additional, Höps, Wolfram, additional, Benito-Garagorri, Eva, additional, Hasenfeld, Patrick, additional, Korbel, Jan O., additional, Mahmoud, Medhat, additional, Paulin, Luis F., additional, Jhangiani, Shalini N., additional, Muzny, Donna M., additional, Fatih, Jawid M., additional, Gibbs, Richard A., additional, Pendleton, Matthew, additional, Harrington, Eoghan, additional, Juul, Sissel, additional, Lindstrand, Anna, additional, Sedlazeck, Fritz J., additional, Pehlivan, Davut, additional, Lupski, James R., additional, and Carvalho, Claudia M.B., additional

Published
2023
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27. De novo variants in H3-3A and H3-3B are associated with neurodevelopmental delay, dysmorphic features, and structural brain abnormalities

Author

Okur, Volkan, Chen, Zefu, Vossaert, Liesbeth, Peacock, Sandra, Rosenfeld, Jill, Zhao, Lina, Du, Haowei, Calamaro, Emily, Gerard, Amanda, Zhao, Sen, Kelsay, Jill, Lahr, Ashley, Mighton, Chloe, Porter, Hillary M., Siemon, Amy, Silver, Josh, Svihovec, Shayna, Fong, Chin-To, Grant, Christina L., Lerner-Ellis, Jordan, Manickam, Kandamurugu, Madan-Khetarpal, Suneeta, McCandless, Shawn E., Morel, Chantal F., Schaefer, G. Bradley, Berry-Kravis, Elizabeth M., Gates, Ryan, Gomez-Ospina, Natalia, Qiu, Guixing, Zhang, Terry Jianguo, Wu, Zhihong, Meng, Linyan, Liu, Pengfei, Scott, Daryl A., Lupski, James R., Eng, Christine M., Wu, Nan, and Yuan, Bo

Published
2021
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28. Biallelic missense variants in COG3 cause a congenital disorder of glycosylation with impairment of retrograde vesicular trafficking

Author

Duan, Ruizhi, primary, Marafi, Dana, additional, Xia, Zhi‐Jie, additional, Ng, Bobby G., additional, Maroofian, Reza, additional, Sumya, Farhana Taher, additional, Saad, Ahmed K., additional, Du, Haowei, additional, Fatih, Jawid M., additional, Hunter, Jill V., additional, Elbendary, Hasnaa M., additional, Baig, Shahid M., additional, Abdullah, Uzma, additional, Ali, Zafar, additional, Efthymiou, Stephanie, additional, Murphy, David, additional, Mitani, Tadahiro, additional, Withers, Marjorie A., additional, Jhangiani, Shalini N., additional, Coban‐Akdemir, Zeynep, additional, Calame, Daniel G., additional, Pehlivan, Davut, additional, Gibbs, Richard A., additional, Posey, Jennifer E., additional, Houlden, Henry, additional, Lupashin, Vladimir V., additional, Zaki, Maha S., additional, Freeze, Hudson H., additional, and Lupski, James R., additional

Published
2023
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30. Genomic Balancing Act: deciphering DNA rearrangements in the complex chromosomal aberration involving 5p15.2, 2q31.1, and 18q21.32

Author

Dardas, Zain, Marafi, Dana, Duan, Ruizhi, Fatih, Jawid M., El-Rashidy, Omnia F., Grochowski, Christopher M., Carvalho, Claudia M. B., Jhangiani, Shalini N., Bi, Weimin, Du, Haowei, Gibbs, Richard A., Posey, Jennifer E., Calame, Daniel G., Zaki, Maha S., and Lupski, James R.

Abstract

Despite extensive research into the genetic underpinnings of neurodevelopmental disorders (NDD), many clinical cases remain unresolved. We studied a female proband with a NDD, mildly dysmorphic facial features, and brain stem hypoplasia on neuroimaging. Comprehensive genomic analyses revealed a terminal 5p loss and a terminal 18q gain in the proband while a diploid copy number for chromosomes 5 and 18 in both parents. Genomic investigations in the proband identified an unbalanced translocation t(5;18) with additional genetic material from chromosome 2 (2q31.3) inserted at the breakpoint, pointing to a complex chromosomal rearrangement (CCR) involving 5p15.2, 2q31.3, and 18q21.32. Breakpoint junction analyses enabled by long-read genome sequencing unveiled the presence of four distinct junctions in the father, who is a carrier of a balanced CCR. The proband inherited from the father both the abnormal chromosome 5 resulting in segmental aneusomies of chr5 (loss) and chr18 (gain) and a der(2) homologue. Evidences suggest a chromoplexy mechanism for this CCR derivation, involving double-strand breaks (DSBs) repaired by non-homologous end joining (NHEJ) or alternative end joining (alt-EJ). The complexity of the CCR and the segregation of homologues elucidate the genetic model for this family. This study demonstrates the importance of combining multiple genomic technologies to uncover genetic causes of complex neurodevelopmental syndromes and to better understand genetic disease mechanisms.

Published
2024
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32. A biallelic frameshift indel in PPP1R35 as a cause of primary microcephaly

Author

Dawood, Moez, primary, Akay, Gulsen, additional, Mitani, Tadahiro, additional, Marafi, Dana, additional, Fatih, Jawid M., additional, Gezdirici, Alper, additional, Najmabadi, Hossein, additional, Kahrizi, Kimia, additional, Punetha, Jaya, additional, Grochowski, Christopher M., additional, Du, Haowei, additional, Jolly, Angad, additional, Li, He, additional, Coban‐Akdemir, Zeynep, additional, Sedlazeck, Fritz J., additional, Hunter, Jill V., additional, Jhangiani, Shalini N., additional, Muzny, Donna, additional, Pehlivan, Davut, additional, Posey, Jennifer E., additional, Carvalho, Claudia M. B., additional, Gibbs, Richard A., additional, and Lupski, James R., additional

Published
2023
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36. Developmental genomics of limb malformations: Allelic series in association with gene dosage effects contribute to the clinical variability

Author

Duan, Ruizhi, primary, Hijazi, Hadia, additional, Gulec, Elif Yilmaz, additional, Eker, Hatice Koçak, additional, Costa, Silvia R., additional, Sahin, Yavuz, additional, Ocak, Zeynep, additional, Isikay, Sedat, additional, Ozalp, Ozge, additional, Bozdogan, Sevcan, additional, Aslan, Huseyin, additional, Elcioglu, Nursel, additional, Bertola, Débora R., additional, Gezdirici, Alper, additional, Du, Haowei, additional, Fatih, Jawid M., additional, Grochowski, Christopher M., additional, Akay, Gulsen, additional, Jhangiani, Shalini N., additional, Karaca, Ender, additional, Gu, Shen, additional, Coban-Akdemir, Zeynep, additional, Posey, Jennifer E., additional, Bayram, Yavuz, additional, Sutton, V. Reid, additional, Carvalho, Claudia M.B., additional, Pehlivan, Davut, additional, Gibbs, Richard A., additional, and Lupski, James R., additional

Published
2022
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37. A reverse genetics and genomics approach to gene paralog function and disease: Myokymia and the juxtaparanode

Author

Marafi, Dana, primary, Kozar, Nina, additional, Duan, Ruizhi, additional, Bradley, Stephen, additional, Yokochi, Kenji, additional, Al Mutairi, Fuad, additional, Saadi, Nebal Waill, additional, Whalen, Sandra, additional, Brunet, Theresa, additional, Kotzaeridou, Urania, additional, Choukair, Daniela, additional, Keren, Boris, additional, Nava, Caroline, additional, Kato, Mitsuhiro, additional, Arai, Hiroshi, additional, Froukh, Tawfiq, additional, Faqeih, Eissa Ali, additional, AlAsmari, Ali M., additional, Saleh, Mohammed M., additional, Pinto e Vairo, Filippo, additional, Pichurin, Pavel N., additional, Klee, Eric W., additional, Schmitz, Christopher T., additional, Grochowski, Christopher M., additional, Mitani, Tadahiro, additional, Herman, Isabella, additional, Calame, Daniel G., additional, Fatih, Jawid M., additional, Du, Haowei, additional, Coban-Akdemir, Zeynep, additional, Pehlivan, Davut, additional, Jhangiani, Shalini N., additional, Gibbs, Richard A., additional, Miyatake, Satoko, additional, Matsumoto, Naomichi, additional, Wagstaff, Laura J., additional, Posey, Jennifer E., additional, Lupski, James R., additional, Meijer, Dies, additional, and Wagner, Matias, additional

Published
2022
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38. Back Cover, Volume 43, Issue 7

Author

Lima, Ariadne R., primary, Ferreira, Barbara M., additional, Zhang, Chaofan, additional, Jolly, Angad, additional, Du, Haowei, additional, White, Janson J., additional, Dawood, Moez, additional, Lins, Tulio C., additional, Chiabai, Marcela A., additional, van Beusekom, Ellen, additional, Cordoba, Mara S., additional, Caldas Rosa, Erica C.C., additional, Kayserili, Hulya, additional, Kimonis, Virginia, additional, Wu, Erica, additional, Mellado, Cecilia, additional, Aggarwal, Vineet, additional, Richieri‐Costa, Antonio, additional, Brunoni, Décio, additional, Canó, Talyta M., additional, Jorge, Alexander A. L., additional, Kim, Chong A., additional, Honjo, Rachel, additional, Bertola, Débora R., additional, Dandalo‐Girardi, Raissa M., additional, Bayram, Yavuz, additional, Gezdirici, Alper, additional, Yilmaz‐Gulec, Elif, additional, Gumus, Evren, additional, Yilmaz, Gülay C., additional, Okamoto, Nobuhiko, additional, Ohashi, Hirofumi, additional, Coban–Akdemir, Zeynep, additional, Mitani, Tadahiro, additional, Jhangiani, Shalini N., additional, Muzny, Donna M., additional, Regattieri, Neysa A.P., additional, Pogue, Robert, additional, Pereira, Rinaldo W., additional, Otto, Paulo A., additional, Gibbs, Richard A., additional, Ali, Bassam R., additional, van Bokhoven, Hans, additional, Brunner, Han G., additional, Sutton, V. Reid, additional, Lupski, James R., additional, Vianna‐Morgante, Angela M., additional, Carvalho, Claudia M. B., additional, and Mazzeu, Juliana F., additional

Published
2022
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39. Biallelic Variants in the Ectonucleotidase ENTPD1 Cause a Complex Neurodevelopmental Disorder with Intellectual Disability, Distinct White Matter Abnormalities, and Spastic Paraplegia

Author

Calame, Daniel G., primary, Herman, Isabella, additional, Maroofian, Reza, additional, Marshall, Aren E., additional, Donis, Karina Carvalho, additional, Fatih, Jawid M., additional, Mitani, Tadahiro, additional, Du, Haowei, additional, Grochowski, Christopher M., additional, Sousa, Sergio B., additional, Gijavanekar, Charul, additional, Bakhtiari, Somayeh, additional, Ito, Yoko A., additional, Rocca, Clarissa, additional, Hunter, Jill V., additional, Sutton, V. Reid, additional, Emrick, Lisa T., additional, Boycott, Kym M., additional, Lossos, Alexander, additional, Fellig, Yakov, additional, Prus, Eugenia, additional, Kalish, Yosef, additional, Meiner, Vardiella, additional, Suerink, Manon, additional, Ruivenkamp, Claudia, additional, Muirhead, Kayla, additional, Saadi, Nebal W., additional, Zaki, Maha S., additional, Bouman, Arjan, additional, Barakat, Tahsin Stefan, additional, Skidmore, David L., additional, Osmond, Matthew, additional, Silva, Thiago Oliveira, additional, Murphy, David, additional, Karimiani, Ehsan Ghayoor, additional, Jamshidi, Yalda, additional, Jaddoa, Asaad Ghanim, additional, Tajsharghi, Homa, additional, Jin, Sheng Chih, additional, Abbaszadegan, Mohammad Reza, additional, Ebrahimzadeh‐Vesal, Reza, additional, Hosseini, Susan, additional, Alavi, Shahryar, additional, Bahreini, Amir, additional, Zarean, Elahe, additional, Salehi, Mohammad Mehdi, additional, Al‐Sannaa, Nouriya Abbas, additional, Zifarelli, Giovanni, additional, Bauer, Peter, additional, Robson, Simon C., additional, Coban‐Akdemir, Zeynep, additional, Travaglini, Lorena, additional, Nicita, Francesco, additional, Jhangiani, Shalini N., additional, Gibbs, Richard A., additional, Posey, Jennifer E., additional, Kruer, Michael C., additional, Kernohan, Kristin D., additional, Morales Saute, Jonas A., additional, Houlden, Henry, additional, Vanderver, Adeline, additional, Elsea, Sarah H., additional, Pehlivan, Davut, additional, Marafi, Dana, additional, and Lupski, James R., additional

Published
2022
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40. 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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41. Additional file 1 of The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation

Author

Du, Haowei, Jolly, Angad, Grochowski, Christopher M., Yuan, Bo, Dawood, Moez, Jhangiani, Shalini N., Li, He, Muzny, Donna, Fatih, Jawid M., Coban-Akdemir, Zeynep, Carlin, Mary Esther, Scheuerle, Angela E., Witzl, Karin, Posey, Jennifer E., Pendleton, Matthew, Harrington, Eoghan, Juul, Sissel, Hastings, P. J., Bi, Weimin, Gibbs, Richard A., Sedlazeck, Fritz J., Lupski, James R., Carvalho, Claudia M. B., and Liu, Pengfei

Abstract

Additional file 1. Supplementary methods, clinical description of BAB9637, BAB3097, and BAB9484, Table S1, S3, S5, S6, Figure S1-S9.

Published
2022
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42. Novel RETREG1 (FAM134B)founder allele is linked to HSAN2B and renal disease in a Turkish family

Author

Taşdelen, Elifcan, primary, Calame, Daniel G., additional, Akay, Gulsen, additional, Mitani, Tadahiro, additional, Fatih, Jawid M., additional, Herman, Isabella, additional, Du, Haowei, additional, Coban‐Akdemir, Zeynep, additional, Marafi, Dana, additional, Jhangiani, Shalini N., additional, Posey, Jennifer E., additional, Gibbs, Richard A., additional, Altıparmak, Taylan, additional, Kutlay, Nüket Yürür, additional, Lupski, James R., additional, and Pehlivan, Davut, additional

Published
2022
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43. Retrospective analysis of a clinical exome sequencing cohort reveals the mutational spectrum and identifies candidate disease–associated loci for BAFopathies

Author

Chen, Chun-An, primary, Lattier, John, additional, Zhu, Wenmiao, additional, Rosenfeld, Jill, additional, Wang, Lei, additional, Scott, Tiana M., additional, Du, Haowei, additional, Patel, Vipulkumar, additional, Dang, Anh, additional, Magoulas, Pilar, additional, Streff, Haley, additional, Sebastian, Jessica, additional, Svihovec, Shayna, additional, Curry, Kathryn, additional, Delgado, Mauricio R., additional, Hanchard, Neil A., additional, Lalani, Seema, additional, Marom, Ronit, additional, Madan-Khetarpal, Suneeta, additional, Saenz, Margarita, additional, Dai, Hongzheng, additional, Meng, Linyan, additional, Xia, Fan, additional, Bi, Weimin, additional, Liu, Pengfei, additional, Posey, Jennifer E., additional, Scott, Daryl A., additional, Lupski, James R., additional, Eng, Christine M., additional, Xiao, Rui, additional, and Yuan, Bo, additional

Published
2022
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44. Quantitative dissection of multilocus pathogenic variation in an Egyptian infant with severe neurodevelopmental disorder resulting from multiple molecular diagnoses

Author

Herman, Isabella, primary, Jolly, Angad, additional, Du, Haowei, additional, Dawood, Moez, additional, Abdel‐Salam, Ghada M. H., additional, Marafi, Dana, additional, Mitani, Tadahiro, additional, Calame, Daniel G., additional, Coban‐Akdemir, Zeynep, additional, Fatih, Jawid M., additional, Hegazy, Ibrahim, additional, Jhangiani, Shalini N., additional, Gibbs, Richard A., additional, Pehlivan, Davut, additional, Posey, Jennifer E., additional, and Lupski, James R., additional

Published
2021
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45. Expanding the phenotypic and allelic spectrum ofSMG8: Clinical observations reveal overlap withSMG9 ‐associated disease trait

Author

Abdel‐Salam, Ghada M. H., primary, Duan, Ruizhi, additional, Abdel‐Hamid, Mohamed S., additional, Sayed, Inas S. M., additional, Jhangiani, Shalini N., additional, Khan, Ziad, additional, Du, Haowei, additional, Gibbs, Richard A., additional, Posey, Jennifer E., additional, Marafi, Dana, additional, and Lupski, James R., additional

Published
2021
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46. Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy

Author

Marafi, Dana, primary, Fatih, Jawid M, additional, Kaiyrzhanov, Rauan, additional, Ferla, Matteo P, additional, Gijavanekar, Charul, additional, Al-Maraghi, Aljazi, additional, Liu, Ning, additional, Sites, Emily, additional, Alsaif, Hessa S, additional, Al-Owain, Mohammad, additional, Zakkariah, Mohamed, additional, El-Anany, Ehab, additional, Guliyeva, Ulviyya, additional, Guliyeva, Sughra, additional, Gaba, Colette, additional, Haseeb, Ateeq, additional, Alhashem, Amal M, additional, Danish, Enam, additional, Karageorgou, Vasiliki, additional, Beetz, Christian, additional, Subhi, Alaa A, additional, Mullegama, Sureni V, additional, Torti, Erin, additional, Sebastin, Monisha, additional, Breilyn, Margo Sheck, additional, Duberstein, Susan, additional, Abdel-Hamid, Mohamed S, additional, Mitani, Tadahiro, additional, Du, Haowei, additional, Rosenfeld, Jill A, additional, Jhangiani, Shalini N, additional, Coban Akdemir, Zeynep, additional, Gibbs, Richard A, additional, Taylor, Jenny C, additional, Fakhro, Khalid A, additional, Hunter, Jill V, additional, Pehlivan, Davut, additional, Zaki, Maha S, additional, Gleeson, Joseph G, additional, Maroofian, Reza, additional, Houlden, Henry, additional, Posey, Jennifer E, additional, Sutton, V Reid, additional, Alkuraya, Fowzan S, additional, Elsea, Sarah H, additional, and Lupski, James R, additional

Published
2021
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47. High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population

Author

Mitani, Tadahiro, primary, Isikay, Sedat, additional, Gezdirici, Alper, additional, Gulec, Elif Yilmaz, additional, Punetha, Jaya, additional, Fatih, Jawid M., additional, Herman, Isabella, additional, Akay, Gulsen, additional, Du, Haowei, additional, Calame, Daniel G., additional, Ayaz, Akif, additional, Tos, Tulay, additional, Yesil, Gozde, additional, Aydin, Hatip, additional, Geckinli, Bilgen, additional, Elcioglu, Nursel, additional, Candan, Sukru, additional, Sezer, Ozlem, additional, Erdem, Haktan Bagis, additional, Gul, Davut, additional, Demiral, Emine, additional, Elmas, Muhsin, additional, Yesilbas, Osman, additional, Kilic, Betul, additional, Gungor, Serdal, additional, Ceylan, Ahmet C., additional, Bozdogan, Sevcan, additional, Ozalp, Ozge, additional, Cicek, Salih, additional, Aslan, Huseyin, additional, Yalcintepe, Sinem, additional, Topcu, Vehap, additional, Bayram, Yavuz, additional, Grochowski, Christopher M., additional, Jolly, Angad, additional, Dawood, Moez, additional, Duan, Ruizhi, additional, Jhangiani, Shalini N., additional, Doddapaneni, Harsha, additional, Hu, Jianhong, additional, Muzny, Donna M., additional, Marafi, Dana, additional, Akdemir, Zeynep Coban, additional, Karaca, Ender, additional, Carvalho, Claudia M.B., additional, Gibbs, Richard A., additional, Posey, Jennifer E., additional, Lupski, James R., additional, and Pehlivan, Davut, additional

Published
2021
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48. Deep clinicopathological phenotyping identifies a previously unrecognized pathogenic EMD splice variant

Author

Calame, Daniel G., primary, Fatih, Jawid M., additional, Herman, Isabella, additional, Coban‐Akdemir, Zeynep, additional, Du, Haowei, additional, Mitani, Tadahiro, additional, Jhangiani, Shalini N., additional, Marafi, Dana, additional, Gibbs, Richard A., additional, Posey, Jennifer E., additional, Mehta, Vidya P., additional, Mohila, Carrie A., additional, Abid, Farida, additional, Lotze, Timothy E., additional, Pehlivan, Davut, additional, Adesina, Adekunle M., additional, and Lupski, James R., additional

Published
2021
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49. An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates

Author

Mc Cartney, Ann M., primary, Mahmoud, Medhat, additional, Jochum, Michael, additional, Agustinho, Daniel Paiva, additional, Zorman, Barry, additional, Al Khleifat, Ahmad, additional, Dabbaghie, Fawaz, additional, K Kesharwani, Rupesh, additional, Smolka, Moritz, additional, Dawood, Moez, additional, Albin, Dreycey, additional, Aliyev, Elbay, additional, Almabrazi, Hakeem, additional, Arslan, Ahmed, additional, Balaji, Advait, additional, Behera, Sairam, additional, Billingsley, Kimberley, additional, L Cameron, Daniel, additional, Daw, Joyjit, additional, T. Dawson, Eric, additional, De Coster, Wouter, additional, Du, Haowei, additional, Dunn, Christopher, additional, Esteban, Rocio, additional, Jolly, Angad, additional, Kalra, Divya, additional, Liao, Chunxiao, additional, Liu, Yunxi, additional, Lu, Tsung-Yu, additional, M Havrilla, James, additional, M Khayat, Michael, additional, Marin, Maximillian, additional, Monlong, Jean, additional, Price, Stephen, additional, Rafael Gener, Alejandro, additional, Ren, Jingwen, additional, Sagayaradj, Sagayamary, additional, Sapoval, Nicolae, additional, Sinner, Claude, additional, C. Soto, Daniela, additional, Soylev, Arda, additional, Subramaniyan, Arun, additional, Syed, Najeeb, additional, Tadimeti, Neha, additional, Tater, Pamella, additional, Vats, Pankaj, additional, Vaughn, Justin, additional, Walker, Kimberly, additional, Wang, Gaojianyong, additional, Zeng, Qiandong, additional, Zhang, Shangzhe, additional, Zhao, Tingting, additional, Kille, Bryce, additional, Biederstedt, Evan, additional, Chaisson, Mark, additional, English, Adam, additional, Kronenberg, Zev, additional, J. Treangen, Todd, additional, Hefferon, Timothy, additional, Chin, Chen-Shan, additional, Busby, Ben, additional, and J Sedlazeck, Fritz, additional

Published
2021
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50. Novel RETREG1 (FAM134B) founder allele is linked to HSAN2B and renal disease in a Turkish family.

Author

Taşdelen, Elifcan, Calame, Daniel G., Akay, Gulsen, Mitani, Tadahiro, Fatih, Jawid M., Herman, Isabella, Du, Haowei, Coban‐Akdemir, Zeynep, Marafi, Dana, Jhangiani, Shalini N., Posey, Jennifer E., Gibbs, Richard A., Altıparmak, Taylan, Kutlay, Nüket Yürür, Lupski, James R., and Pehlivan, Davut

Abstract

Hereditary sensory and autonomic neuropathy type 2B (HSAN2B) is a rare autosomal recessive peripheral neuropathy caused by biallelic variants in RETREG1 (formerly FAM134B). HSAN2B is characterized by sensory impairment resulting in skin ulcerations, amputations, and osteomyelitis as well as variable weakness, spasticity, and autonomic dysfunction. Here, we report four affected individuals with recurrent osteomyelitis, ulceration, and amputation of hands and feet, sensory neuropathy, hyperhidrosis, urinary incontinence, and renal failure from a family without any known shared parental ancestry. Due to the history of chronic recurrent multifocal osteomyelitis and microcytic anemia, a diagnosis of Majeed syndrome was considered; however, sequencing of LPIN2 was negative. Family‐based exome sequencing (ES) revealed a novel homozygous ultrarare RETREG1 variant NM_001034850.2:c.321G>A;p.Trp107Ter. Electrophysiological studies of the proband demonstrated axonal sensorimotor neuropathy predominantly in the lower extremities. Consistent with the lack of shared ancestry, the coefficient of inbreeding calculated from ES data was low (F = 0.002), but absence of heterozygosity (AOH) analysis demonstrated a 7.2 Mb AOH block surrounding the variant consistent with a founder allele. Two of the four affected individuals had unexplained renal failure which has not been reported in HSAN2B cases to date. Therefore, this report describes a novel RETREG1 founder allele and suggests renal failure may be an unrecognized feature of the RETREG1‐disease spectrum. [ABSTRACT FROM AUTHOR]

Published
2022
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