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1. Implementation, Evolution, and Laboratory Performance of Methods-Based Proficiency Testing for Next-Generation Sequencing Detection of Germline Sequence Variants

Author

Tsuchiya, Karen D., Funke, Birgit, Hegde, Madhuri, Santani, Avni, Souers, Rhona J., Szelinger, Szabolcs, Halley, Jaimie, Zhao, Qin, Mot, Nicole, Roy, Angshumoy, Smith, Vanessa L., Zhang, Bing M., Voelkerding, Karl, and Moyer, Ann M.

Subjects
Nucleotide sequencing -- Usage -- Quality management, DNA sequencing -- Usage -- Quality management, Genetic variation -- Identification and classification, Health
Abstract

* Context.--Next-generation sequencing (NGS)-based assays are used for diagnosis of diverse inherited disorders. Limited data are available pertaining to interlaboratory analytical performance of these assays. Objective.--To report on the College of American Pathologists (CAP) NGS Germline Program, which is methods based, and explore the evolution in laboratory testing practices. Design.--Results from the NGS Germline Program from 2016-2020 were analyzed for interlaboratory analytical performance. Self-reported laboratory testing practices were also evaluated. Results.--From 2016-2020, a total of 297 laboratories participated in at least 1 program mailing. Of the 289 laboratories that provided information on tests offered, 138 (47.8%) offered only panel testing throughout their enrollment, while 35 (12.1%) offered panels and exome testing, 30 (10.4%) offered only exomes, 9 (3.1%) offered only genomes, and 15 (5.2%) offered panels, exomes, and genomes. The remainder (62 laboratories, 21.4%) changed their test offerings during the 2016-2020 timeframe. Considering each genomic position/interval, the median detection percentage at variant positions across the 2016-2020 mailings ranged from 94.3% to 100%, while at reference positions (no variant detected), the median correct response percentage was 100% across all mailings. When considering performance of individual laboratories, 89.5% (136 of 152) to 98.0% (149 of 152) of laboratories successfully met the detection threshold ([greater than or equal to] 90% of the variants present), while 94.6% (87 of 92) to 100% (163 of 163) of laboratories met the 95% specificity threshold across mailings. Conclusions.--Since the inception of this program, laboratories have consistently performed well. The median sensitivity and specificity of detection of sequence variants included in this program (eg, single nucleotide variants, insertions, and deletions) were 100.0%. doi: 10.5858/arpa.2023-0090-CP), Next-generation sequencing (NGS)-based tests are of higher complexity than most traditional molecular tests owing to the interrogation of many positions simultaneously, as well as requirements for extensive laboratory wet bench [...]

Published
2024
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5. Object recognition via echoes: quantifying the crossmodal transfer of three-dimensional shape information between echolocation, vision, and haptics

Author

Santani Teng, Caroline Danforth, Nickolas Paternoster, Michael Ezeana, and Amrita Puri

Subjects
echolocation, blindness, object perception, crossmodal perception, spatial resolution, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract

Active echolocation allows blind individuals to explore their surroundings via self-generated sounds, similarly to dolphins and other echolocating animals. Echolocators emit sounds, such as finger snaps or mouth clicks, and parse the returning echoes for information about their surroundings, including the location, size, and material composition of objects. Because a crucial function of perceiving objects is to enable effective interaction with them, it is important to understand the degree to which three-dimensional shape information extracted from object echoes is useful in the context of other modalities such as haptics or vision. Here, we investigated the resolution of crossmodal transfer of object-level information between acoustic echoes and other senses. First, in a delayed match-to-sample task, blind expert echolocators and sighted control participants inspected common (everyday) and novel target objects using echolocation, then distinguished the target object from a distractor using only haptic information. For blind participants, discrimination accuracy was overall above chance and similar for both common and novel objects, whereas as a group, sighted participants performed above chance for the common, but not novel objects, suggesting that some coarse object information (a) is available to both expert blind and novice sighted echolocators, (b) transfers from auditory to haptic modalities, and (c) may be facilitated by prior object familiarity and/or material differences, particularly for novice echolocators. Next, to estimate an equivalent resolution in visual terms, we briefly presented blurred images of the novel stimuli to sighted participants (N = 22), who then performed the same haptic discrimination task. We found that visuo-haptic discrimination performance approximately matched echo-haptic discrimination for a Gaussian blur kernel σ of ~2.5°. In this way, by matching visual and echo-based contributions to object discrimination, we can estimate the quality of echoacoustic information that transfers to other sensory modalities, predict theoretical bounds on perception, and inform the design of assistive techniques and technology available for blind individuals.

Published
2024
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6. Mitochondrial genome sequence analysis: A custom bioinformatics pipeline substantially improves Affymetrix MitoChip v2.0 call rate and accuracy

Author

Xie Hongbo M, Perin Juan C, Schurr Theodore G, Dulik Matthew C, Zhadanov Sergey I, Baur Joseph A, King Michael P, Place Emily, Clarke Colleen, Grauer Michael, Schug Jonathan, Santani Avni, Albano Anthony, Kim Cecilia, Procaccio Vincent, Hakonarson Hakon, Gai Xiaowu, and Falk Marni J

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Mitochondrial genome sequence analysis is critical to the diagnostic evaluation of mitochondrial disease. Existing methodologies differ widely in throughput, complexity, cost efficiency, and sensitivity of heteroplasmy detection. Affymetrix MitoChip v2.0, which uses a sequencing-by-genotyping technology, allows potentially accurate and high-throughput sequencing of the entire human mitochondrial genome to be completed in a cost-effective fashion. However, the relatively low call rate achieved using existing software tools has limited the wide adoption of this platform for either clinical or research applications. Here, we report the design and development of a custom bioinformatics software pipeline that achieves a much improved call rate and accuracy for the Affymetrix MitoChip v2.0 platform. We used this custom pipeline to analyze MitoChip v2.0 data from 24 DNA samples representing a broad range of tissue types (18 whole blood, 3 skeletal muscle, 3 cell lines), mutations (a 5.8 kilobase pair deletion and 6 known heteroplasmic mutations), and haplogroup origins. All results were compared to those obtained by at least one other mitochondrial DNA sequence analysis method, including Sanger sequencing, denaturing HPLC-based heteroduplex analysis, and/or the Illumina Genome Analyzer II next generation sequencing platform. Results An average call rate of 99.75% was achieved across all samples with our custom pipeline. Comparison of calls for 15 samples characterized previously by Sanger sequencing revealed a total of 29 discordant calls, which translates to an estimated 0.012% for the base call error rate. We successfully identified 4 known heteroplasmic mutations and 24 other potential heteroplasmic mutations across 20 samples that passed quality control. Conclusions Affymetrix MitoChip v2.0 analysis using our optimized MitoChip Filtering Protocol (MFP) bioinformatics pipeline now offers the high sensitivity and accuracy needed for reliable, high-throughput and cost-efficient whole mitochondrial genome sequencing. This approach provides a viable alternative of potential utility for both clinical diagnostic and research applications to traditional Sanger and other emerging sequencing technologies for whole mitochondrial genome analysis.

Published
2011
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8. Paperless and Contactless Operations in Distribution Services

Author

Tendulkar, Parmanand P., Santani, Devendra H., Pujari, Nikhil H., Jadhav, Pramod B., Dalvi, Amit C., Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, 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, Möller, Sebastian, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, 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, Zhang, Junjie James, Series Editor, Pillai, Reji Kumar, editor, Singh, B. P., editor, and Murugesan, N., editor

Published
2022
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10. Known pathogenic gene variants and new candidates detected in sudden unexpected infant death using whole genome sequencing.

Author

Bard, Angela M., Clark, Lindsay V., Cosgun, Erdal, Aldinger, Kimberly A., Timms, Andrew, Quina, Lely A., Ferres, Juan M. Lavista, Jardine, David, Haas, Elisabeth A., Becker, Tatiana M., Pagan, Chelsea M., Santani, Avni, Martinez, Diego, Barua, Soumitra, McNutt, Zakkary, Nesbitt, Addie, Mitchell, Edwin A., and Ramirez, Jan‐Marino

Abstract

The purpose of this study is to gain insights into potential genetic factors contributing to the infant's vulnerability to Sudden Unexpected Infant Death (SUID). Whole Genome Sequencing (WGS) was performed on 144 infants that succumbed to SUID, and 573 healthy adults. Variants were filtered by gnomAD allele frequencies and predictions of functional consequences. Variants of interest were identified in 88 genes, in 64.6% of our cohort. Seventy‐three of these have been previously associated with SIDS/SUID/SUDP. Forty‐three can be characterized as cardiac genes and are related to cardiomyopathies, arrhythmias, and other conditions. Variants in 22 genes were associated with neurologic functions. Variants were also found in 13 genes reported to be pathogenic for various systemic disorders and in two genes associated with immunological function. Variants in eight genes are implicated in the response to hypoxia and the regulation of reactive oxygen species (ROS) and have not been previously described in SIDS/SUID/SUDP. Seventy‐two infants met the triple risk hypothesis criteria. Our study confirms and further expands the list of genetic variants associated with SUID. The abundance of genes associated with heart disease and the discovery of variants associated with the redox metabolism have important mechanistic implications for the pathophysiology of SUID. [ABSTRACT FROM AUTHOR]

Published
2024
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11. NFIB Haploinsufficiency Is Associated with Intellectual Disability and Macrocephaly

Author

Schanze, Ina, Bunt, Jens, Lim, Jonathan WC, Schanze, Denny, Dean, Ryan J, Alders, Marielle, Blanchet, Patricia, Attié-Bitach, Tania, Berland, Siren, Boogert, Steven, Boppudi, Sangamitra, Bridges, Caitlin J, Cho, Megan T, Dobyns, William B, Donnai, Dian, Douglas, Jessica, Earl, Dawn L, Edwards, Timothy J, Faivre, Laurence, Fregeau, Brieana, Genevieve, David, Gérard, Marion, Gatinois, Vincent, Holder-Espinasse, Muriel, Huth, Samuel F, Izumi, Kosuke, Kerr, Bronwyn, Lacaze, Elodie, Lakeman, Phillis, Mahida, Sonal, Mirzaa, Ghayda M, Morgan, Sian M, Nowak, Catherine, Peeters, Hilde, Petit, Florence, Pilz, Daniela T, Puechberty, Jacques, Reinstein, Eyal, Rivière, Jean-Baptiste, Santani, Avni B, Schneider, Anouck, Sherr, Elliott H, Smith-Hicks, Constance, Wieland, Ilse, Zackai, Elaine, Zhao, Xiaonan, Gronostajski, Richard M, Zenker, Martin, and Richards, Linda J

Subjects
Biomedical and Clinical Sciences, Mental Health, Pediatric, Intellectual and Developmental Disabilities (IDD), Neurosciences, Rare Diseases, Behavioral and Social Science, Genetics, Brain Disorders, Aetiology, 2.1 Biological and endogenous factors, Mental health, Neurological, Adolescent, Adult, Animals, Cerebral Cortex, Child, Child, Preschool, Codon, Nonsense, Cohort Studies, Corpus Callosum, Female, Haploinsufficiency, Humans, Intellectual Disability, Male, Megalencephaly, Mice, Mice, Knockout, NFI Transcription Factors, Polymorphism, Single Nucleotide, Young Adult, NFIB, agenesis of the corpus callosum, chromosome 9p22.3, chromosome 9p23, developmental delay, haploinsufficiency, intellectual disability, macrocephaly, megalencephaly, nuclear factor I, Biological Sciences, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

The nuclear factor I (NFI) family of transcription factors play an important role in normal development of multiple organs. Three NFI family members are highly expressed in the brain, and deletions or sequence variants in two of these, NFIA and NFIX, have been associated with intellectual disability (ID) and brain malformations. NFIB, however, has not previously been implicated in human disease. Here, we present a cohort of 18 individuals with mild ID and behavioral issues who are haploinsufficient for NFIB. Ten individuals harbored overlapping microdeletions of the chromosomal 9p23-p22.2 region, ranging in size from 225 kb to 4.3 Mb. Five additional subjects had point sequence variations creating a premature termination codon, and three subjects harbored single-nucleotide variations resulting in an inactive protein as determined using an in vitro reporter assay. All individuals presented with additional variable neurodevelopmental phenotypes, including muscular hypotonia, motor and speech delay, attention deficit disorder, autism spectrum disorder, and behavioral abnormalities. While structural brain anomalies, including dysgenesis of corpus callosum, were variable, individuals most frequently presented with macrocephaly. To determine whether macrocephaly could be a functional consequence of NFIB disruption, we analyzed a cortex-specific Nfib conditional knockout mouse model, which is postnatally viable. Utilizing magnetic resonance imaging and histology, we demonstrate that Nfib conditional knockout mice have enlargement of the cerebral cortex but preservation of overall brain structure and interhemispheric connectivity. Based on our findings, we propose that haploinsufficiency of NFIB causes ID with macrocephaly.

Published
2018

13. Phenotypic expansion of CACNA1C-associated disorders to include isolated neurological manifestations

Author

Rodan, Lance H., Spillmann, Rebecca C., Kurata, Harley T., Lamothe, Shawn M., Maghera, Jasmine, Jamra, Rami Abou, Alkelai, Anna, Antonarakis, Stylianos E., Atallah, Isis, Bar-Yosef, Omer, Bilan, Frédéric, Bjorgo, Kathrine, Blanc, Xavier, Van Bogaert, Patrick, Bolkier, Yoav, Burrage, Lindsay C., Christ, Björn U., Granadillo, Jorge L., Dickson, Patricia, Donald, Kirsten A., Dubourg, Christèle, Eliyahu, Aviva, Emrick, Lisa, Engleman, Kendra, Gonfiantini, Michaela Veronika, Good, Jean-Marc, Kalser, Judith, Kloeckner, Chiara, Lachmeijer, Guus, Macchiaiolo, Marina, Nicita, Francesco, Odent, Sylvie, O’Heir, Emily, Ortiz-Gonzalez, Xilma, Pacio-Miguez, Marta, Palomares-Bralo, María, Pena, Loren, Platzer, Konrad, Quinodoz, Mathieu, Ranza, Emmanuelle, Rosenfeld, Jill A., Roulet-Perez, Eliane, Santani, Avni, Santos-Simarro, Fernando, Pode-Shakked, Ben, Skraban, Cara, Slaugh, Rachel, Superti-Furga, Andrea, Thiffault, Isabelle, van Jaabrsveld, Richard H., Vincent, Marie, Wang, Hong-Gang, Zacher, Pia, Alejandro, Mercedes E., Azamian, Mahshid S., Bacino, Carlos A., Balasubramanyam, Ashok, Chao, Hsiao-Tuan, Clark, Gary D., Craigen, William J., Dai, Hongzheng, Dhar, Shweta U., Emrick, Lisa T., Goldman, Alica M., Hanchard, Neil A., Jamal, Fariha, Karaviti, Lefkothea, Lalani, Seema R., Lee, Brendan H., Lewis, Richard A., Marom, Ronit, Moretti, Paolo M., Murdock, David R., Nicholas, Sarah K., Orengo, James P., Posey, Jennifer E., Potocki, Lorraine, Samson, Susan L., Scott, Daryl A., Tran, Alyssa A., Vogel, Tiphanie P., Wangler, Michael F., Yamamoto, Shinya, Eng, Christine M., Liu, Pengfei, Ward, Patricia A., Behrens, Edward, Deardorff, Matthew, Falk, Marni, Hassey, Kelly, Sullivan, Kathleen, Vanderver, Adeline, Goldstein, David B., Cope, Heidi, McConkie-Rosell, Allyn, Schoch, Kelly, Shashi, Vandana, Smith, Edward C., Sullivan, Jennifer A., Tan, Queenie K.-G., Walley, Nicole M., Agrawal, Pankaj B., Beggs, Alan H., Berry, Gerard T., Briere, Lauren C., Cobban, Laurel A., Coggins, Matthew, Cooper, Cynthia M., Fieg, Elizabeth L., High, Frances, Holm, Ingrid A., Korrick, Susan, Krier, Joel B., Lincoln, Sharyn A., Loscalzo, Joseph, Maas, Richard L., MacRae, Calum A., Pallais, J. Carl, Rao, Deepak A., Silverman, Edwin K., Stoler, Joan M., Sweetser, David A., Walker, Melissa, Walsh, Chris A., Esteves, Cecilia, Kelley, Emily G., Kohane, Isaac S., LeBlanc, Kimberly, McCray, Alexa T., Nagy, Anna, Dasari, Surendra, Lanpher, Brendan C., Lanza, Ian R., Morava, Eva, Oglesbee, Devin, Bademci, Guney, Barbouth, Deborah, Bivona, Stephanie, Carrasquillo, Olveen, Chang, Ta Chen Peter, Forghani, Irman, Grajewski, Alana, Isasi, Rosario, Lam, Byron, Levitt, Roy, Liu, Xue Zhong, McCauley, Jacob, Sacco, Ralph, Saporta, Mario, Schaechter, Judy, Tekin, Mustafa, Telischi, Fred, Thorson, Willa, Zuchner, Stephan, Colley, Heather A., Dayal, Jyoti G., Eckstein, David J., Findley, Laurie C., Krasnewich, Donna M., Mamounas, Laura A., Manolio, Teri A., Mulvihill, John J., LaMoure, Grace L., Goldrich, Madison P., Urv, Tiina K., Doss, Argenia L., Acosta, Maria T., Bonnenmann, Carsten, D’Souza, Precilla, Draper, David D., Ferreira, Carlos, Godfrey, Rena A., Groden, Catherine A., Macnamara, Ellen F., Maduro, Valerie V., Markello, Thomas C., Nath, Avi, Novacic, Donna, Pusey, Barbara N., Toro, Camilo, Wahl, Colleen E., Baker, Eva, Burke, Elizabeth A., Adams, David R., Gahl, William A., Malicdan, May Christine V., Tifft, Cynthia J., Wolfe, Lynne A., Yang, John, Power, Bradley, Gochuico, Bernadette, Huryn, Laryssa, Latham, Lea, Davis, Joie, Mosbrook-Davis, Deborah, Rossignol, Francis, Ben Solomon, MacDowall, John, Thurm, Audrey, Zein, Wadih, Yousef, Muhammad, Adam, Margaret, Amendola, Laura, Bamshad, Michael, Beck, Anita, Bennett, Jimmy, Berg-Rood, Beverly, Blue, Elizabeth, Boyd, Brenna, Byers, Peter, Chanprasert, Sirisak, Cunningham, Michael, Dipple, Katrina, Doherty, Daniel, Earl, Dawn, Glass, Ian, Golden-Grant, Katie, Hahn, Sihoun, Hing, Anne, Hisama, Fuki M., Horike-Pyne, Martha, Jarvik, Gail P., Jarvik, Jeffrey, Jayadev, Suman, Lam, Christina, Maravilla, Kenneth, Mefford, Heather, Merritt, J. Lawrence, Mirzaa, Ghayda, Nickerson, Deborah, Raskind, Wendy, Rosenwasser, Natalie, Scott, C. Ron, Sun, Angela, Sybert, Virginia, Wallace, Stephanie, Wener, Mark, Wenger, Tara, Ashley, Euan A., Bejerano, Gill, Bernstein, Jonathan A., Bonner, Devon, Coakley, Terra R., Fernandez, Liliana, Fisher, Paul G., Fresard, Laure, Hom, Jason, Huang, Yong, Kohler, Jennefer N., Kravets, Elijah, Majcherska, Marta M., Martin, Beth A., Marwaha, Shruti, McCormack, Colleen E., Raja, Archana N., Reuter, Chloe M., Ruzhnikov, Maura, Sampson, Jacinda B., Smith, Kevin S., Sutton, Shirley, Tabor, Holly K., Tucker, Brianna M., Wheeler, Matthew T., Zastrow, Diane B., Zhao, Chunli, Byrd, William E., Crouse, Andrew B., Might, Matthew, Nakano-Okuno, Mariko, Whitlock, Jordan, Brown, Gabrielle, Butte, Manish J., Dell’Angelica, Esteban C., Dorrani, Naghmeh, Douine, Emilie D., Fogel, Brent L., Gutierrez, Irma, Huang, Alden, Krakow, Deborah, Lee, Hane, Loo, Sandra K., Mak, Bryan C., Martin, Martin G., Martínez-Agosto, Julian A., McGee, Elisabeth, Nelson, Stanley F., Nieves-Rodriguez, Shirley, Palmer, Christina G.S., Papp, Jeanette C., Parker, Neil H., Renteria, Genecee, Signer, Rebecca H., Sinsheimer, Janet S., Wan, Jijun, Wang, Lee-kai, Perry, Katherine Wesseling, Woods, Jeremy D., Alvey, Justin, Andrews, Ashley, Bale, Jim, Bohnsack, John, Botto, Lorenzo, Carey, John, Pace, Laura, Longo, Nicola, Marth, Gabor, Moretti, Paolo, Quinlan, Aaron, Velinder, Matt, Viskochil, Dave, Bayrak-Toydemir, Pinar, Mao, Rong, Westerfield, Monte, Bican, Anna, Brokamp, Elly, Duncan, Laura, Hamid, Rizwan, Kennedy, Jennifer, Kozuira, Mary, Newman, John H., PhillipsIII, John A., Rives, Lynette, Robertson, Amy K., Solem, Emily, Cogan, Joy D., Cole, F. Sessions, Hayes, Nichole, Kiley, Dana, Sisco, Kathy, Wambach, Jennifer, Wegner, Daniel, Baldridge, Dustin, Pak, Stephen, Schedl, Timothy, Shin, Jimann, Solnica-Krezel, Lilianna, Rush, Eric, Pitt, Geoffrey S., and Au, Ping Yee Billie

Published
2021
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14. Neptune: an environment for the delivery of genomic medicine

Author

Eric, Venner, Yi, Victoria, Murdock, David, Kalla, Sara E., Wu, Tsung-Jung, Sabo, Aniko, Li, Shoudong, Meng, Qingchang, Tian, Xia, Murugan, Mullai, Cohen, Michelle, Kovar, Christie, Wei, Wei-Qi, Chung, Wendy K., Weng, Chunhua, Wiesner, Georgia L., Jarvik, Gail P., Muzny, Donna, Gibbs, Richard A., Abrams, Debra, Adunyah, Samuel E., Albertson-Junkans, Ladia, Almoguera, Berta, Ames, Darren C., Appelbaum, Paul, Aronson, Samuel, Aufox, Sharon, Babb, Lawrence J., Balasubramanian, Adithya, Bangash, Hana, Basford, Melissa, Bastarache, Lisa, Baxter, Samantha, Behr, Meckenzie, Benoit, Barbara, Bhoj, Elizabeth, Bielinski, Suzette J., Bland, Harris T., Blout, Carrie, Borthwick, Kenneth, Bottinger, Erwin P., Bowser, Mark, Brand, Harrison, Brilliant, Murray, Brodeur, Wendy, Caraballo, Pedro, Carrell, David, Carroll, Andrew, Castillo, Lisa, Castro, Victor, Chandanavelli, Gauthami, Chiang, Theodore, Chisholm, Rex L., Christensen, Kurt D., Chung, Wendy, Chute, Christopher G., City, Brittany, Cobb, Beth L., Connolly, John J., Crane, Paul, Crew, Katherine, Crosslin, David R., Dayal, Jyoti, De Andrade, Mariza, De la Cruz, Jessica, Denny, Josh C., Denson, Shawn, DeSmet, Tim, Dikilitas, Ozan, Dinsmore, Michael J., Dodge, Sheila, Dunlea, Phil, Edwards, Todd L., Eng, Christine M., Fasel, David, Fedotov, Alex, Feng, Qiping, Fleharty, Mark, Foster, Andrea, Freimuth, Robert, Friedrich, Christopher, Fullerton, Stephanie M., Funke, Birgit, Gabriel, Stacey, Gainer, Vivian, Gharavi, Ali, Glazer, Andrew M., Glessner, Joseph T., Goehringer, Jessica, Gordon, Adam S., Graham, Chet, Green, Robert C., Gundelach, Justin H., Hain, Heather S., Hakonarson, Hakon, Harden, Maegan V., Harley, John, Harr, Margaret, Hartzler, Andrea, Hayes, M. Geoffrey, Hebbring, Scott, Henrikson, Nora, Hershey, Andrew, Hoell, Christin, Holm, Ingrid, Howell, Kayla M., Hripcsak, George, Hu, Jianhong, Hynes, Elizabeth Duffy, Jayaseelan, Joy C., Jiang, Yunyun, Joo, Yoonjung Yoonie, Jose, Sheethal, Josyula, Navya Shilpa, Justice, Anne E., Kalra, Divya, Karlson, Elizabeth W., Keating, Brendan J., Kelly, Melissa A., Kenny, Eimear E., Key, Dustin, Kiryluk, Krzysztof, Kitchner, Terrie, Klanderman, Barbara, Klee, Eric, Kochan, David C., Korchina, Viktoriya, Kottyan, Leah, Kudalkar, Emily, Rahm, Alanna Kulchak, Kullo, Iftikhar J., Lammers, Philip, Larson, Eric B., Lebo, Matthew S., Leduc, Magalie, Lee, Ming Ta (Michael), Lennon, Niall J., Leppig, Kathleen A., Leslie, Nancy D., Li, Rongling, Liang, Wayne H., Lin, Chiao-Feng, Linder, Jodell E., Lindor, Noralane M., Lingren, Todd, Linneman, James G., Liu, Cong, Liu, Wen, Liu, Xiuping, Lynch, John, Lyon, Hayley, Macbeth, Alyssa, Mahadeshwar, Harshad, Mahanta, Lisa, Malin, Bradley, Manolio, Teri, Marasa, Maddalena, Marsolo, Keith, McGowan, Michelle L., McNally, Elizabeth, Meldrim, Jim, Mentch, Frank, Rasouly, Hila Milo, Mosley, Jonathan, Mukherjee, Shubhabrata, Mullen, Thomas E., Muniz, Jesse, Murdock, David R., Murphy, Shawn, Myers, Melanie F., Namjou, Bahram, Ni, Yizhao, Onofrio, Robert C., Obeng, Aniwaa Owusu, Person, Thomas N., Peterson, Josh F., Petukhova, Lynn, Pisieczko, Cassandra J., Pratap, Siddharth, Prows, Cynthia A., Puckelwartz, Megan J., Raj, Ritika, Ralston, James D., Ramaprasan, Arvind, Ramirez, Andrea, Rasmussen, Luke, Rasmussen-Torvik, Laura, Raychaudhuri, Soumya, Rehm, Heidi L., Ritchie, Marylyn D., Rives, Catherine, Riza, Beenish, Roden, Dan M., Rosenthal, Elisabeth A., Santani, Avni, Dan, Schaid, Scherer, Steven, Scott, Stuart, Scrol, Aaron, Sengupta, Soumitra, Shang, Ning, Sharma, Himanshu, Sharp, Richard R., Singh, Rajbir, Sleiman, Patrick M.A., Slowik, Kara, Smith, Joshua C., Smith, Maureen E., Smoot, Duane T., Smoller, Jordan W., Sohn, Sunghwan, Stanaway, Ian B., Starren, Justin, Stroud, Mary, Su, Jessica, Taylor, Casey Overby, Tolwinski, Kasia, Van Driest, Sara L., Vargas, Sean M., Varugheese, Matthew, Veenstra, David, Venner, Eric, Verbitsky, Miguel, Vicente, Gina, Wagner, Michael, Walker, Kimberly, Walunas, Theresa, Wang, Liwen, Wang, Qiaoyan, Weiss, Scott T., Wells, Quinn S., White, Peter S., Wiley, Ken L., Jr, Williams, Janet L., Williams, Marc S., Wilson, Michael W., Witkowski, Leora, Woods, Laura Allison, Woolf, Betty, Wynn, Julia, Yang, Yaping, Zhang, Ge, Zhang, Lan, and Zouk, Hana

Published
2021
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15. De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability

Author

Küry, Sébastien, van Woerden, Geeske M, Besnard, Thomas, Onori, Martina Proietti, Latypova, Xénia, Towne, Meghan C, Cho, Megan T, Prescott, Trine E, Ploeg, Melissa A, Sanders, Stephan, Stessman, Holly AF, Pujol, Aurora, Distel, Ben, Robak, Laurie A, Bernstein, Jonathan A, Denommé-Pichon, Anne-Sophie, Lesca, Gaëtan, Sellars, Elizabeth A, Berg, Jonathan, Carré, Wilfrid, Busk, Øyvind Løvold, van Bon, Bregje WM, Waugh, Jeff L, Deardorff, Matthew, Hoganson, George E, Bosanko, Katherine B, Johnson, Diana S, Dabir, Tabib, Holla, Øystein Lunde, Sarkar, Ajoy, Tveten, Kristian, de Bellescize, Julitta, Braathen, Geir J, Terhal, Paulien A, Grange, Dorothy K, van Haeringen, Arie, Lam, Christina, Mirzaa, Ghayda, Burton, Jennifer, Bhoj, Elizabeth J, Douglas, Jessica, Santani, Avni B, Nesbitt, Addie I, Helbig, Katherine L, Andrews, Marisa V, Begtrup, Amber, Tang, Sha, van Gassen, Koen LI, Juusola, Jane, Foss, Kimberly, Enns, Gregory M, Moog, Ute, Hinderhofer, Katrin, Paramasivam, Nagarajan, Lincoln, Sharyn, Kusako, Brandon H, Lindenbaum, Pierre, Charpentier, Eric, Nowak, Catherine B, Cherot, Elouan, Simonet, Thomas, Ruivenkamp, Claudia AL, Hahn, Sihoun, Brownstein, Catherine A, Xia, Fan, Schmitt, Sébastien, Deb, Wallid, Bonneau, Dominique, Nizon, Mathilde, Quinquis, Delphine, Chelly, Jamel, Rudolf, Gabrielle, Sanlaville, Damien, Parent, Philippe, Gilbert-Dussardier, Brigitte, Toutain, Annick, Sutton, Vernon R, Thies, Jenny, Peart-Vissers, Lisenka ELM, Boisseau, Pierre, Vincent, Marie, Grabrucker, Andreas M, Dubourg, Christèle, Network, Undiagnosed Diseases, Tan, Wen-Hann, Verbeek, Nienke E, Granzow, Martin, Santen, Gijs WE, Shendure, Jay, Isidor, Bertrand, Pasquier, Laurent, Redon, Richard, Yang, Yaping, State, Matthew W, Kleefstra, Tjitske, Cogné, Benjamin, HUGO, GEM, Study, Deciphering Developmental Disorders, Petrovski, Slavé, and Retterer, Kyle

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Neurosciences, Brain Disorders, Genetics, Intellectual and Developmental Disabilities (IDD), Pediatric, Underpinning research, 1.1 Normal biological development and functioning, Aetiology, 2.1 Biological and endogenous factors, Neurological, Animals, Brain, Calcium-Calmodulin-Dependent Protein Kinase Type 2, Cell Line, Exome, Female, Glutamic Acid, HEK293 Cells, Humans, Intellectual Disability, Male, Mice, Mice, Inbred C57BL, Mutation, Neurons, Phosphorylation, Signal Transduction, Undiagnosed Diseases Network, GEM HUGO, Deciphering Developmental Disorders Study, AMPAR, CAMK2, CAMK2A, CAMK2B, NMDAR, de novo mutations, intellectual disability, synaptic plasticity, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Calcium/calmodulin-dependent protein kinase II (CAMK2) is one of the first proteins shown to be essential for normal learning and synaptic plasticity in mice, but its requirement for human brain development has not yet been established. Through a multi-center collaborative study based on a whole-exome sequencing approach, we identified 19 exceedingly rare de novo CAMK2A or CAMK2B variants in 24 unrelated individuals with intellectual disability. Variants were assessed for their effect on CAMK2 function and on neuronal migration. For both CAMK2A and CAMK2B, we identified mutations that decreased or increased CAMK2 auto-phosphorylation at Thr286/Thr287. We further found that all mutations affecting auto-phosphorylation also affected neuronal migration, highlighting the importance of tightly regulated CAMK2 auto-phosphorylation in neuronal function and neurodevelopment. Our data establish the importance of CAMK2A and CAMK2B and their auto-phosphorylation in human brain function and expand the phenotypic spectrum of the disorders caused by variants in key players of the glutamatergic signaling pathway.

Published
2017

16. WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features

Author

Skraban, Cara M, Wells, Constance F, Markose, Preetha, Cho, Megan T, Nesbitt, Addie I, Au, PY Billie, Begtrup, Amber, Bernat, John A, Bird, Lynne M, Cao, Kajia, de Brouwer, Arjan PM, Denenberg, Elizabeth H, Douglas, Ganka, Gibson, Kristin M, Grand, Katheryn, Goldenberg, Alice, Innes, A Micheil, Juusola, Jane, Kempers, Marlies, Kinning, Esther, Markie, David M, Owens, Martina M, Payne, Katelyn, Person, Richard, Pfundt, Rolph, Stocco, Amber, Turner, Claire LS, Verbeek, Nienke E, Walsh, Laurence E, Warner, Taylor C, Wheeler, Patricia G, Wieczorek, Dagmar, Wilkens, Alisha B, Zonneveld-Huijssoon, Evelien, Study, Deciphering Developmental Disorders, Kleefstra, Tjitske, Robertson, Stephen P, Santani, Avni, van Gassen, Koen LI, and Deardorff, Matthew A

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Dental/Oral and Craniofacial Disease, Rare Diseases, Neurodegenerative, Epilepsy, Clinical Research, Pediatric, Intellectual and Developmental Disabilities (IDD), Brain Disorders, Neurosciences, 2.1 Biological and endogenous factors, Aetiology, Adaptor Proteins, Signal Transducing, Amino Acid Sequence, Base Sequence, Child, Preschool, Chromosome Deletion, Facies, Female, Gait, Growth and Development, Haploinsufficiency, Humans, Intellectual Disability, Male, Mutation, Proteins, RNA Stability, Seizures, Syndrome, Deciphering Developmental Disorders Study, WD-40, WDR protein, WDR26, intellectual disability, seizure, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

We report 15 individuals with de novo pathogenic variants in WDR26. Eleven of the individuals carry loss-of-function mutations, and four harbor missense substitutions. These 15 individuals comprise ten females and five males, and all have intellectual disability with delayed speech, a history of febrile and/or non-febrile seizures, and a wide-based, spastic, and/or stiff-legged gait. These subjects share a set of common facial features that include a prominent maxilla and upper lip that readily reveal the upper gingiva, widely spaced teeth, and a broad nasal tip. Together, these features comprise a recognizable facial phenotype. We compared these features with those of chromosome 1q41q42 microdeletion syndrome, which typically contains WDR26, and noted that clinical features are consistent between the two subsets, suggesting that haploinsufficiency of WDR26 contributes to the pathology of 1q41q42 microdeletion syndrome. Consistent with this, WDR26 loss-of-function single-nucleotide mutations identified in these subjects lead to nonsense-mediated decay with subsequent reduction of RNA expression and protein levels. We derived a structural model of WDR26 and note that missense variants identified in these individuals localize to highly conserved residues of this WD-40-repeat-containing protein. Given that WDR26 mutations have been identified in ∼1 in 2,000 of subjects in our clinical cohorts and that WDR26 might be poorly annotated in exome variant-interpretation pipelines, we would anticipate that this disorder could be more common than currently appreciated.

Published
2017

17. A survey of current practices for genomic sequencing test interpretation and reporting processes in US laboratories.

Author

O'Daniel, Julianne M, McLaughlin, Heather M, Amendola, Laura M, Bale, Sherri J, Berg, Jonathan S, Bick, David, Bowling, Kevin M, Chao, Elizabeth C, Chung, Wendy K, Conlin, Laura K, Cooper, Gregory M, Das, Soma, Deignan, Joshua L, Dorschner, Michael O, Evans, James P, Ghazani, Arezou A, Goddard, Katrina A, Gornick, Michele, Farwell Hagman, Kelly D, Hambuch, Tina, Hegde, Madhuri, Hindorff, Lucia A, Holm, Ingrid A, Jarvik, Gail P, Knight Johnson, Amy, Mighion, Lindsey, Morra, Massimo, Plon, Sharon E, Punj, Sumit, Richards, C Sue, Santani, Avni, Shirts, Brian H, Spinner, Nancy B, Tang, Sha, Weck, Karen E, Wolf, Susan M, Yang, Yaping, and Rehm, Heidi L

Subjects
Disclosure, Genetic Testing: methods, standards, Humans, Incidental Findings, Information Dissemination, Laboratories: ethics, standards, Practice Guidelines as Topic, Research Report, Sample Size, Sequence Analysis, DNA: methods, standards, Surveys and Questionnaires
Abstract

While the diagnostic success of genomic sequencing expands, the complexity of this testing should not be overlooked. Numerous laboratory processes are required to support the identification, interpretation, and reporting of clinically significant variants. This study aimed to examine the workflow and reporting procedures among US laboratories to highlight shared practices and identify areas in need of standardization.Surveys and follow-up interviews were conducted with laboratories offering exome and/or genome sequencing to support a research program or for routine clinical services. The 73-item survey elicited multiple choice and free-text responses that were later clarified with phone interviews.Twenty-one laboratories participated. Practices highly concordant across all groups included consent documentation, multiperson case review, and enabling patient opt-out of incidental or secondary findings analysis. Noted divergence included use of phenotypic data to inform case analysis and interpretation and reporting of case-specific quality metrics and methods. Few laboratory policies detailed procedures for data reanalysis, data sharing, or patient access to data.This study provides an overview of practices and policies of experienced exome and genome sequencing laboratories. The results enable broader consideration of which practices are becoming standard approaches, where divergence remains, and areas of development in best practice guidelines that may be helpful.Genet Med advance online publication 03 Novemeber 2016.

Published
2017

19. CommuniSense: Crowdsourcing Road Hazards in Nairobi

Author

Santani, Darshan, Njuguna, Jidraph, Bills, Tierra, Bryant, Aisha W., Bryant, Reginald, Ledgard, Jonathan, and Gatica-Perez, Daniel

Subjects
Computer Science - Computers and Society
Abstract

Nairobi is one of the fastest growing metropolitan cities and a major business and technology powerhouse in Africa. However, Nairobi currently lacks monitoring technologies to obtain reliable data on traffic and road infrastructure conditions. In this paper, we investigate the use of mobile crowdsourcing as means to gather and document Nairobi's road quality information. We first present the key findings of a city-wide road quality survey about the perception of existing road quality conditions in Nairobi. Based on the survey's findings, we then developed a mobile crowdsourcing application, called CommuniSense, to collect road quality data. The application serves as a tool for users to locate, describe, and photograph road hazards. We tested our application through a two-week field study amongst 30 participants to document various forms of road hazards from different areas in Nairobi. To verify the authenticity of user-contributed reports from our field study, we proposed to use online crowdsourcing using Amazon's Mechanical Turk (MTurk) to verify whether submitted reports indeed depict road hazards. We found 92% of user-submitted reports to match the MTurkers judgements. While our prototype was designed and tested on a specific city, our methodology is applicable to other developing cities., Comment: In Proceedings of 17th International Conference on Human-Computer Interaction with Mobile Devices and Services (MobileHCI 2015)

Published
2015

26. Loud and Trendy: Crowdsourcing Impressions of Social Ambiance in Popular Indoor Urban Places

Author

Santani, Darshan and Gatica-Perez, Daniel

Subjects
Computer Science - Social and Information Networks, Physics - Physics and Society
Abstract

New research cutting across architecture, urban studies, and psychology is contextualizing the understanding of urban spaces according to the perceptions of their inhabitants. One fundamental construct that relates place and experience is ambiance, which is defined as "the mood or feeling associated with a particular place". We posit that the systematic study of ambiance dimensions in cities is a new domain for which multimedia research can make pivotal contributions. We present a study to examine how images collected from social media can be used for the crowdsourced characterization of indoor ambiance impressions in popular urban places. We design a crowdsourcing framework to understand suitability of social images as data source to convey place ambiance, to examine what type of images are most suitable to describe ambiance, and to assess how people perceive places socially from the perspective of ambiance along 13 dimensions. Our study is based on 50,000 Foursquare images collected from 300 popular places across six cities worldwide. The results show that reliable estimates of ambiance can be obtained for several of the dimensions. Furthermore, we found that most aggregate impressions of ambiance are similar across popular places in all studied cities. We conclude by presenting a multidisciplinary research agenda for future research in this domain.

Published
2014
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27. The CHD4-related syndrome: a comprehensive investigation of the clinical spectrum, genotype–phenotype correlations, and molecular basis

Author

Weiss, Karin, Lazar, Hayley P., Kurolap, Alina, Martinez, Ariel F., Paperna, Tamar, Cohen, Lior, Smeland, Marie F., Whalen, Sandra, Heide, Solveig, Keren, Boris, Terhal, Pauline, Irving, Melita, Takaku, Motoki, Roberts, John D., Petrovich, Robert M., Schrier Vergano, Samantha A., Kenney, Amy, Hove, Hanne, DeChene, Elizabeth, Quinonez, Shane C., Colin, Estelle, Ziegler, Alban, Rumple, Melissa, Jain, Mahim, Monteil, Danielle, Roeder, Elizabeth R., Nugent, Kimberly, van Haeringen, Arie, Gambello, Michael, Santani, Avni, Medne, Līvija, Krock, Bryan, Skraban, Cara M., Zackai, Elaine H., Dubbs, Holly A., Smol, Thomas, Ghoumid, Jamal, Parker, Michael J., Wright, Michael, Turnpenny, Peter, Clayton-Smith, Jill, Metcalfe, Kay, Kurumizaka, Hitoshi, Gelb, Bruce D., Baris Feldman, Hagit, Campeau, Philippe M., Muenke, Maximilian, Wade, Paul A., and Lachlan, Katherine

Published
2020
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29. A Device for Human Ultrasonic Echolocation

Author

Sohl-Dickstein, Jascha, Teng, Santani, Gaub, Benjamin M, Rodgers, Chris C, Li, Crystal, DeWeese, Michael R, and Harper, Nicol S

Subjects
Assistive Technology, Rehabilitation, Clinical Research, Bioengineering, Neurosciences, Adult, Animals, Ear Auricle, Echolocation, Equipment Design, Female, Humans, Male, Models, Biological, Self-Help Devices, Signal Processing, Computer-Assisted, Ultrasonics, Visually Impaired Persons, Young Adult, Assistive device, blind, echolocation, ultrasonic, Artificial Intelligence and Image Processing, Biomedical Engineering, Electrical and Electronic Engineering
Abstract

ObjectiveWe present a device that combines principles of ultrasonic echolocation and spatial hearing to provide human users with environmental cues that are 1) not otherwise available to the human auditory system, and 2) richer in object and spatial information than the more heavily processed sonar cues of other assistive devices. The device consists of a wearable headset with an ultrasonic emitter and stereo microphones with affixed artificial pinnae. The goal of this study is to describe the device and evaluate the utility of the echoic information it provides.MethodsThe echoes of ultrasonic pulses were recorded and time stretched to lower their frequencies into the human auditory range, then played back to the user. We tested performance among naive and experienced sighted volunteers using a set of localization experiments, in which the locations of echo-reflective surfaces were judged using these time-stretched echoes.ResultsNaive subjects were able to make laterality and distance judgments, suggesting that the echoes provide innately useful information without prior training. Naive subjects were generally unable to make elevation judgments from recorded echoes. However, trained subjects demonstrated an ability to judge elevation as well.ConclusionThis suggests that the device can be used effectively to examine the environment and that the human auditory system can rapidly adapt to these artificial echolocation cues.SignificanceInterpreting and interacting with the external world constitutes a major challenge for persons who are blind or visually impaired. This device has the potential to aid blind people in interacting with their environment.

Published
2015

30. Actionable exomic incidental findings in 6503 participants: challenges of variant classification

Author

Amendola, Laura M, Dorschner, Michael O, Robertson, Peggy D, Salama, Joseph S, Hart, Ragan, Shirts, Brian H, Murray, Mitzi L, Tokita, Mari J, Gallego, Carlos J, Kim, Daniel Seung, Bennett, James T, Crosslin, David R, Ranchalis, Jane, Jones, Kelly L, Rosenthal, Elisabeth A, Jarvik, Ella R, Itsara, Andy, Turner, Emily H, Herman, Daniel S, Schleit, Jennifer, Burt, Amber, Jamal, Seema M, Abrudan, Jenica L, Johnson, Andrew D, Conlin, Laura K, Dulik, Matthew C, Santani, Avni, Metterville, Danielle R, Kelly, Melissa, Foreman, Ann Katherine M, Lee, Kristy, Taylor, Kent D, Guo, Xiuqing, Crooks, Kristy, Kiedrowski, Lesli A, Raffel, Leslie J, Gordon, Ora, Machini, Kalotina, Desnick, Robert J, Biesecker, Leslie G, Lubitz, Steven A, Mulchandani, Surabhi, Cooper, Greg M, Joffe, Steven, Richards, C Sue, Yang, Yaoping, Rotter, Jerome I, Rich, Stephen S, O’Donnell, Christopher J, Berg, Jonathan S, Spinner, Nancy B, Evans, James P, Fullerton, Stephanie M, Leppig, Kathleen A, Bennett, Robin L, Bird, Thomas, Sybert, Virginia P, Grady, William M, Tabor, Holly K, Kim, Jerry H, Bamshad, Michael J, Wilfond, Benjamin, Motulsky, Arno G, Scott, C Ronald, Pritchard, Colin C, Walsh, Tom D, Burke, Wylie, Raskind, Wendy H, Byers, Peter, Hisama, Fuki M, Rehm, Heidi, Nickerson, Debbie A, and Jarvik, Gail P

Subjects
Biological Sciences, Genetics, Biotechnology, Human Genome, Clinical Research, Good Health and Well Being, Adult, Black People, Exome, Female, Gene Frequency, Genes, Dominant, Genetic Association Studies, Genetic Testing, Genome, Human, Genomics, High-Throughput Nucleotide Sequencing, Humans, Incidental Findings, Male, Phenotype, Polymorphism, Single Nucleotide, White People, Medical and Health Sciences, Bioinformatics
Abstract

Recommendations for laboratories to report incidental findings from genomic tests have stimulated interest in such results. In order to investigate the criteria and processes for assigning the pathogenicity of specific variants and to estimate the frequency of such incidental findings in patients of European and African ancestry, we classified potentially actionable pathogenic single-nucleotide variants (SNVs) in all 4300 European- and 2203 African-ancestry participants sequenced by the NHLBI Exome Sequencing Project (ESP). We considered 112 gene-disease pairs selected by an expert panel as associated with medically actionable genetic disorders that may be undiagnosed in adults. The resulting classifications were compared to classifications from other clinical and research genetic testing laboratories, as well as with in silico pathogenicity scores. Among European-ancestry participants, 30 of 4300 (0.7%) had a pathogenic SNV and six (0.1%) had a disruptive variant that was expected to be pathogenic, whereas 52 (1.2%) had likely pathogenic SNVs. For African-ancestry participants, six of 2203 (0.3%) had a pathogenic SNV and six (0.3%) had an expected pathogenic disruptive variant, whereas 13 (0.6%) had likely pathogenic SNVs. Genomic Evolutionary Rate Profiling mammalian conservation score and the Combined Annotation Dependent Depletion summary score of conservation, substitution, regulation, and other evidence were compared across pathogenicity assignments and appear to have utility in variant classification. This work provides a refined estimate of the burden of adult onset, medically actionable incidental findings expected from exome sequencing, highlights challenges in variant classification, and demonstrates the need for a better curated variant interpretation knowledge base.

Published
2015

31. Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network

Author

Zouk, Hana, Venner, Eric, Lennon, Niall J., Muzny, Donna M., Abrams, Debra, Adunyah, Samuel, Albertson-Junkans, Ladia, Ames, Darren C., Appelbaum, Paul, Aronson, Samuel, Aufox, Sharon, Babb, Lawrence J., Balasubramanian, Adithya, Bangash, Hana, Basford, Melissa, Bastarache, Lisa, Baxter, Samantha, Behr, Meckenzie, Benoit, Barbara, Bhoj, Elizabeth, Bielinski, Suzette J., Bland, Sarah T., Blout, Carrie, Borthwick, Kenneth, Bottinger, Erwin P., Bowser, Mark, Brand, Harrison, Brilliant, Murray, Brodeur, Wendy, Caraballo, Pedro, Carrell, David, Carroll, Andrew, Almoguera, Berta, Castillo, Lisa, Castro, Victor, Chandanavelli, Gauthami, Chiang, Theodore, Chisholm, Rex L., Christensen, Kurt D., Chung, Wendy, Chute, Christopher G., City, Brittany, Cobb, Beth L., Connolly, John J., Crane, Paul, Crew, Katherine, Crosslin, David, De Andrade, Mariza, De la Cruz, Jessica, Denson, Shawn, Denny, Josh, DeSmet, Tim, Dikilitas, Ozan, Friedrich, Christopher, Fullerton, Stephanie M., Funke, Birgit, Gabriel, Stacey, Gainer, Vivian, Gharavi, Ali, Glazer, Andrew M., Glessner, Joseph T., Goehringer, Jessica, Gordon, Adam S., Graham, Chet, Green, Robert C., Gundelach, Justin H., Dayal, Jyoti, Hain, Heather S., Hakonarson, Hakon, Harden, Maegan V., Harley, John, Harr, Margaret, Hartzler, Andrea, Hayes, M. Geoffrey, Hebbring, Scott, Henrikson, Nora, Hershey, Andrew, Hoell, Christin, Holm, Ingrid, Howell, Kayla M., Hripcsak, George, Hu, Jianhong, Jarvik, Gail P., Jayaseelan, Joy C., Jiang, Yunyun, Joo, Yoonjung Yoonie, Jose, Sheethal, Josyula, Navya Shilpa, Justice, Anne E., Kalla, Sara E., Kalra, Divya, Karlson, Elizabeth, Kelly, Melissa A., Keating, Brendan J., Kenny, Eimear E., Key, Dustin, Kiryluk, Krzysztof, Kitchner, Terrie, Klanderman, Barbara, Klee, Eric, Kochan, David C., Korchina, Viktoriya, Kottyan, Leah, Kovar, Christie, Kudalkar, Emily, Kullo, Iftikhar J., Lammers, Philip, Larson, Eric B., Lebo, Matthew S., Leduc, Magalie, Lee, Ming Ta (Michael), Leppig, Kathleen A., Leslie, Nancy D., Li, Rongling, Liang, Wayne H., Lin, Chiao-Feng, Linder, Jodell, Lindor, Noralane M., Lingren, Todd, Linneman, James G., Liu, Cong, Liu, Wen, Liu, Xiuping, Lynch, John, Lyon, Hayley, Macbeth, Alyssa, Mahadeshwar, Harshad, Mahanta, Lisa, Malin, Brad, Manolio, Teri, Marasa, Maddalena, Marsolo, Keith, Dinsmore, Michael J., Dodge, Sheila, Hynes, Elizabeth Duffy, Dunlea, Phil, Edwards, Todd L., Eng, Christine M., Fasel, David, Fedotov, Alex, Feng, Qiping, Fleharty, Mark, Foster, Andrea, Freimuth, Robert, McGowan, Michelle L., McNally, Elizabeth, Meldrim, Jim, Mentch, Frank, Mosley, Jonathan, Mukherjee, Shubhabrata, Mullen, Thomas E., Muniz, Jesse, Murdock, David R., Murphy, Shawn, Murugan, Mullai, Myers, Melanie F., Namjou, Bahram, Ni, Yizhao, Obeng, Aniwaa Owusu, Onofrio, Robert C., Taylor, Casey Overby, Person, Thomas N., Peterson, Josh F., Petukhova, Lynn, Pisieczko, Cassandra J., Pratap, Siddharth, Prows, Cynthia A., Puckelwartz, Megan J., Rahm, Alanna Kulchak, Raj, Ritika, Ralston, James D., Ramaprasan, Arvind, Ramirez, Andrea, Rasmussen, Luke, Rasmussen-Torvik, Laura, Rasouly, Hila Milo, Raychaudhuri, Soumya, Ritchie, Marylyn D., Rives, Catherine, Riza, Beenish, Roden, Dan, Rosenthal, Elisabeth A., Santani, Avni, Schaid, Dan, Scherer, Steven, Scott, Stuart, Scrol, Aaron, Sengupta, Soumitra, Shang, Ning, Sharma, Himanshu, Sharp, Richard R., Singh, Rajbir, Sleiman, Patrick M.A., Slowik, Kara, Smith, Joshua C., Smith, Maureen E., Smoller, Jordan W., Sohn, Sunghwan, Stanaway, Ian B., Starren, Justin, Stroud, Mary, Su, Jessica, Tolwinski, Kasia, Van Driest, Sara L., Vargas, Sean M., Varugheese, Matthew, Veenstra, David, Verbitsky, Miguel, Vicente, Gina, Wagner, Michael, Walker, Kimberly, Walunas, Theresa, Wang, Liwen, Wang, Qiaoyan, Wei, Wei-Qi, Weiss, Scott T., Wiesner, Georgia L., Wells, Quinn, Weng, Chunhua, White, Peter S., Wiley, Ken L., Jr., Williams, Janet L., Williams, Marc S., Wilson, Michael W., Witkowski, Leora, Woods, Laura Allison, Woolf, Betty, Wu, Tsung-Jung, Wynn, Julia, Yang, Yaping, Yi, Victoria, Zhang, Ge, Zhang, Lan, Rehm, Heidi L., and Gibbs, Richard A.

Published
2019
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32. Inferring Taxi Status Using GPS Trajectories

Author

Zhu, Yin, Zheng, Yu, Zhang, Liuhang, Santani, Darshan, Xie, Xing, and Yang, Qiang

Subjects
Computer Science - Artificial Intelligence, Computer Science - Databases, 68T20, H.2.8
Abstract

In this paper, we infer the statuses of a taxi, consisting of occupied, non-occupied and parked, in terms of its GPS trajectory. The status information can enable urban computing for improving a city's transportation systems and land use planning. In our solution, we first identify and extract a set of effective features incorporating the knowledge of a single trajectory, historical trajectories and geographic data like road network. Second, a parking status detection algorithm is devised to find parking places (from a given trajectory), dividing a trajectory into segments (i.e., sub-trajectories). Third, we propose a two-phase inference model to learn the status (occupied or non-occupied) of each point from a taxi segment. This model first uses the identified features to train a local probabilistic classifier and then carries out a Hidden Semi-Markov Model (HSMM) for globally considering long term travel patterns. We evaluated our method with a large-scale real-world trajectory dataset generated by 600 taxis, showing the advantages of our method over baselines.

Published
2012

33. Molecular insights from comprehensive genomic profiling data in advanced metastatic colorectal cancer in South Asian population: A retrospective observational study.

Author

FATHIMA, NUSRATH, VERMA, KRITHIKA, SUBRAMANYAM, PARIDHY V., MUKHERJEE, NILESH, TANWAR, NISHTHA, JAYARAMAN, SHARANYA, RANGAN, SARANYA, MAHANTI, SHREYA, SAHA, PRABIR, JAVLE, VYOMESH, KHUNTIA, SATYA P., SANTANI, HARSHI, P., ASHWINI, PEDDAGANGANNAGARI, SREEKANTH R., GOWDA, POOJA, VARGHESE, LINU, GORE, ADWAITA, PATEL, AMOL, SAINANI, ANJANA, and KARPE, ASHAY

Published
2024
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35. Implementation, Evolution, and Laboratory Performance of Methods-Based Proficiency Testing for Next-Generation Sequencing Detection of Germline Sequence Variants

Author

Tsuchiya, Karen D., primary, Funke, Birgit, additional, Hegde, Madhuri, additional, Santani, Avni, additional, Souers, Rhona J., additional, Szelinger, Szabolcs, additional, Halley, Jaimie, additional, Zhao, Qin, additional, Mot, Nicole, additional, Roy, Angshumoy, additional, Smith, Vanessa L., additional, Zhang, Bing M., additional, Voelkerding, Karl, additional, and Moyer, Ann M., additional

Published
2023
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36. Survey on Graph DB for Impact Analysis in Payment Platforms

Author

Isha Kanade, Manasi Hatekar, Janvi Santani, rasad Gosavi, and Deepa Sapkal

Subjects
General Medicine
Abstract

Impact analysis is the process of analyzing and predicting the consequences of any changes in the system. This analysis is important because it helps to determine which components get impacted when a component goes down or fails and how the system responds to this change. Payment platforms are a composition of several different components such as CBS, databases and SMS G/W, UPI switches. These components are dependent on each other and work together to perform successful transactions. A graph database (Graph DB) is a database that uses graph structures for storing data. Instead of using tables or documents to represent and store data, it makes use of nodes, edges, and relationships. The nodes of the graph contain the data, and the edges between the nodes show how the data are related to one another. Hence, a graph database can be easily used to represent various components of the payment platform and the relationships between them. Graph database makes it easy to understand the effect of change in one of these components on another.

Published
2023
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40. Development of the Geographical Proportional-to-Size Street-Intercept Sampling (GPSIS) Method for Recruiting Urban Nightlife-Goers in an Entire City

Author

Labhart, Florian, Santani, Darshan, Truong, Jasmine, Tarsetti, Flavio, Bornet, Olivier, Landolt, Sara, Gatica-Perez, Daniel, and Kuntsche, Emmanuel

Abstract

We developed the Geographical Proportional-to-size Street-Intercept Sampling (GPSIS) method in order to obtain a sample of nightlife-goers which accounted for the diversity of spaces, patrons and locations within two Swiss cities. Popular nightlife zones were identified and quantified using social media data and local experts' knowledge. Young people were recruited in the streets on Friday and Saturday nights on three consecutive weekends using the 'fixed-line method, pro-rated for the zone's estimated popularity. Of the 3092 young adults approached, 896 agreed to pre-register. The importance of recruitment in multiple zones and over multiple weekend-days was evidenced by significant variations in participant demographics and registration rates between recruitment zones, times and weather conditions. To conclude, by combining a geographical approach with "in situ" recruitment, GPSIS has considerable potential as a tool for recruiting samples that represent the diversity of the nightlife population and spaces.

Published
2017
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47. Known pathogenic gene variants and new candidates detected in Sudden Unexpected Infant Death (SUID) using Whole Genome Sequencing (WGS)

Author

Ramirez, Jan Marino, primary, Bard, Angela Michelle, additional, Clark, Lindsay V., additional, Cosgun, Erdal, additional, Aldinger, Kimberly A., additional, Timms, Andrew, additional, Quina, Lely A., additional, Lavista Ferres, Juan M, additional, Jardine, David, additional, Haas, Elisabeth A., additional, Becker, Tatiana M., additional, Pagan, Chelsea M., additional, Santani, Avni, additional, Martinez, Diego, additional, Barua, Soumitra, additional, McNutt, Zakkary, additional, and Nesbitt, Addie, additional

Published
2023
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