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JOURNAL ARTICLE
Ali AlMail, Ahmed Jamjoom, Amy Pan, Min Yi Feng, Vann Chau, Alissa M D'Gama, Katherine Howell, Nicole S Y Liang, Amy McTague, Annapurna Poduri, Kimberly Wiltrout, Anne S Bassett, John Christodoulou, Lucie Dupuis, Peter Gill, Tess Levy, Paige Siper, Zornitza Stark, Jacob A S Vorstman, Catherine Diskin, Natalie Jewitt, Danielle Baribeau, Gregory Costain
Genome-wide sequencing and genetic matchmaker services are propelling a new era of genotype-driven ascertainment of novel genetic conditions. The degree to which reported phenotype data in discovery-focused studies address informational priorities for clinicians and families is unclear. We identified reports published from 2017 to 2021 in 10 genetics journals of novel Mendelian disorders. We adjudicated the quality and detail of the phenotype data via 46 questions pertaining to six priority domains: (I) Development, cognition, and mental health; (II) Feeding and growth; (III) Medication use and treatment history; (IV) Pain, sleep, and quality of life; (V) Adulthood; and (VI) Epilepsy...
April 6, 2024: NPJ Genomic Medicine
#2
JOURNAL ARTICLE
Jianbang Chiang, Ziyang Chua, Jia Ying Chan, Ashita Ashish Sule, Wan Hsein Loke, Elaine Lum, Marcus Eng Hock Ong, Nicholas Graves, Joanne Ngeow
Hereditary cancer syndromes constitute approximately 10% of all cancers. Cascade testing involves testing of at-risk relatives to determine if they carry the familial pathogenic variant. Despite growing efforts targeted at improving cascade testing uptake, current literature continues to reflect poor rates of uptake, typically below 30%. This study aims to systematically review current literature on intervention strategies to improve cascade testing, assess the quality of intervention descriptions and evaluate the implementation outcomes of listed interventions...
April 3, 2024: NPJ Genomic Medicine
#3
REVIEW
Tatiane Yanes, Jane Tiller, Casey M Haining, Courtney Wallingford, Margaret Otlowski, Louise Keogh, Aideen McInerney-Leo, Paul Lacaze
No abstract text is available yet for this article.
March 30, 2024: NPJ Genomic Medicine
#4
JOURNAL ARTICLE
K M Ingley, M Zatzman, A M Fontebasso, W Lo, V Subasri, A Goldenberg, Y Li, S Davidson, N Kanwar, L Waldman, L Brunga, Y Babichev, E G Demicco, A Gupta, M Szybowska, S Thipphavong, D Malkin, A Villani, A Shlien, R A Gladdy, R H Kim
Familial gastrointestinal stromal tumors (GIST) are rare. We present a kindred with multiple family members affected with multifocal GIST who underwent whole genome sequencing of the germline and tumor. Affected individuals with GIST harbored a germline variant found within exon 13 of the KIT gene (c.1965T>G; p.Asn655Lys, p.N655K) and a variant in the MSR1 gene (c.877 C > T; p.Arg293*, pR293X). Multifocal GISTs in the proband and her mother were treated with preoperative imatinib, which resulted in severe intolerance...
March 27, 2024: NPJ Genomic Medicine
#5
JOURNAL ARTICLE
Vaidehi Jobanputra, Brock Schroeder, Heidi L Rehm, Wei Shen, Elizabeth Spiteri, Ghunwa Nakouzi, Stacie Taylor, Christian R Marshall, Linyan Meng, Stephen F Kingsmore, Katarzyna Ellsworth, Euan Ashley, Ryan J Taft
No abstract text is available yet for this article.
March 27, 2024: NPJ Genomic Medicine
#6
JOURNAL ARTICLE
Josephina A N Meester, Anne Hebert, Maaike Bastiaansen, Laura Rabaut, Jarl Bastianen, Nele Boeckx, Kathryn Ashcroft, Paldeep S Atwal, Antoine Benichou, Clarisse Billon, Jan D Blankensteijn, Paul Brennan, Stephanie A Bucks, Ian M Campbell, Solène Conrad, Stephanie L Curtis, Majed Dasouki, Carolyn L Dent, James Eden, Himanshu Goel, Verity Hartill, Arjan C Houweling, Bertrand Isidor, Nicola Jackson, Pieter Koopman, Anita Korpioja, Minna Kraatari-Tiri, Liina Kuulavainen, Kelvin Lee, Karen J Low, Alan C Lu, Morgan L McManus, Stephen P Oakley, James Oliver, Nicole M Organ, Eline Overwater, Nicole Revencu, Alison H Trainer, Bhavya Trivedi, Claire L S Turner, Rebecca Whittington, Andreas Zankl, Dominica Zentner, Lut Van Laer, Aline Verstraeten, Bart L Loeys
Pathogenic loss-of-function variants in BGN, an X-linked gene encoding biglycan, are associated with Meester-Loeys syndrome (MRLS), a thoracic aortic aneurysm/dissection syndrome. Since the initial publication of five probands in 2017, we have considerably expanded our MRLS cohort to a total of 18 probands (16 males and 2 females). Segregation analyses identified 36 additional BGN variant-harboring family members (9 males and 27 females). The identified BGN variants were shown to lead to loss-of-function by cDNA and Western Blot analyses of skin fibroblasts or were strongly predicted to lead to loss-of-function based on the nature of the variant...
March 26, 2024: NPJ Genomic Medicine
#7
JOURNAL ARTICLE
Marta Viggiano, Fabiola Ceroni, Paola Visconti, Annio Posar, Maria Cristina Scaduto, Laura Sandoni, Irene Baravelli, Cinzia Cameli, Magali J Rochat, Alessandra Maresca, Alessandro Vaisfeld, Davide Gentilini, Luciano Calzari, Valerio Carelli, Michael C Zody, Elena Maestrini, Elena Bacchelli
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic component in which rare variants contribute significantly to risk. We performed whole genome and/or exome sequencing (WGS and WES) and SNP-array analysis to identify both rare sequence and copy number variants (SNVs and CNVs) in 435 individuals from 116 ASD families. We identified 37 rare potentially damaging de novo SNVs (pdSNVs) in the cases (n = 144). Interestingly, two of them (one stop-gain and one missense variant) occurred in the same gene, BRSK2...
March 22, 2024: NPJ Genomic Medicine
#8
REVIEW
Olaf Riess, Marc Sturm, Benita Menden, Alexandra Liebmann, German Demidov, Dennis Witt, Nicolas Casadei, Jakob Admard, Leon Schütz, Stephan Ossowski, Stacie Taylor, Sven Schaffer, Christopher Schroeder, Andreas Dufke, Tobias Haack
In the era of precision medicine, genome sequencing (GS) has become more affordable and the importance of genomics and multi-omics in clinical care is increasingly being recognized. However, how to scale and effectively implement GS on an institutional level remains a challenge for many. Here, we present Genome First and Ge-Med, two clinical implementation studies focused on identifying the key pillars and processes that are required to make routine GS and predictive genomics a reality in the clinical setting...
March 14, 2024: NPJ Genomic Medicine
#9
JOURNAL ARTICLE
Dhanya Ramachandran, Jonathan P Tyrer, Stefan Kommoss, Anna DeFazio, Marjorie J Riggan, Penelope M Webb, Peter A Fasching, Diether Lambrechts, María J García, Cristina Rodríguez-Antona, Marc T Goodman, Francesmary Modugno, Kirsten B Moysich, Beth Y Karlan, Jenny Lester, Susanne K Kjaer, Allan Jensen, Estrid Høgdall, Ellen L Goode, William A Cliby, Amanika Kumar, Chen Wang, Julie M Cunningham, Stacey J Winham, Alvaro N Monteiro, Joellen M Schildkraut, Daniel W Cramer, Kathryn L Terry, Linda Titus, Line Bjorge, Liv Cecilie Vestrheim Thomsen, Tanja Pejovic, Claus K Høgdall, Iain A McNeish, Taymaa May, David G Huntsman, Jacobus Pfisterer, Ulrich Canzler, Tjoung-Won Park-Simon, Willibald Schröder, Antje Belau, Lars Hanker, Philipp Harter, Jalid Sehouli, Rainer Kimmig, Nikolaus de Gregorio, Barbara Schmalfeldt, Klaus Baumann, Felix Hilpert, Alexander Burges, Boris Winterhoff, Peter Schürmann, Lisa-Marie Speith, Peter Hillemanns, Andrew Berchuck, Sharon E Johnatty, Susan J Ramus, Georgia Chenevix-Trench, Paul D P Pharoah, Thilo Dörk, Florian Heitz
Survival from ovarian cancer depends on the resection status after primary surgery. We performed genome-wide association analyses for resection status of 7705 ovarian cancer patients, including 4954 with high-grade serous carcinoma (HGSOC), to identify variants associated with residual disease. The most significant association with resection status was observed for rs72845444, upstream of MGMT, in HGSOC (p = 3.9 × 10-8 ). In gene-based analyses, PPP2R5C was the most strongly associated gene in HGSOC after stage adjustment...
March 5, 2024: NPJ Genomic Medicine
#10
JOURNAL ARTICLE
Jil D Stegmann, Jeshurun C Kalanithy, Gabriel C Dworschak, Nina Ishorst, Enrico Mingardo, Filipa M Lopes, Yee Mang Ho, Phillip Grote, Tobias T Lindenberg, Öznur Yilmaz, Khadija Channab, Steve Seltzsam, Shirlee Shril, Friedhelm Hildebrandt, Felix Boschann, André Heinen, Angad Jolly, Katherine Myers, Kim McBride, Mir Reza Bekheirnia, Nasim Bekheirnia, Marcello Scala, Manuela Morleo, Vincenzo Nigro, Annalaura Torella, Michele Pinelli, Valeria Capra, Andrea Accogli, Silvia Maitz, Alice Spano, Rory J Olson, Eric W Klee, Brendan C Lanpher, Se Song Jang, Jong-Hee Chae, Philipp Steinbauer, Dietmar Rieder, Andreas R Janecke, Julia Vodopiutz, Ida Vogel, Jenny Blechingberg, Jennifer L Cohen, Kacie Riley, Victoria Klee, Laurence E Walsh, Matthias Begemann, Miriam Elbracht, Thomas Eggermann, Arzu Stoppe, Kyra Stuurman, Marjon van Slegtenhorst, Tahsin Stefan Barakat, Maureen S Mulhern, Tristan T Sands, Cheryl Cytrynbaum, Rosanna Weksberg, Federica Isidori, Tommaso Pippucci, Giulia Severi, Francesca Montanari, Michael C Kruer, Somayeh Bakhtiari, Hossein Darvish, Heiko Reutter, Gregor Hagelueken, Matthias Geyer, Adrian S Woolf, Jennifer E Posey, James R Lupski, Benjamin Odermatt, Alina C Hilger
CELSR3 codes for a planar cell polarity protein. We describe twelve affected individuals from eleven independent families with bi-allelic variants in CELSR3. Affected individuals presented with an overlapping phenotypic spectrum comprising central nervous system (CNS) anomalies (7/12), combined CNS anomalies and congenital anomalies of the kidneys and urinary tract (CAKUT) (3/12) and CAKUT only (2/12). Computational simulation of the 3D protein structure suggests the position of the identified variants to be implicated in penetrance and phenotype expression...
March 1, 2024: NPJ Genomic Medicine
#11
REVIEW
Stephen F Kingsmore, Russell Nofsinger, Kasia Ellsworth
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES...
February 27, 2024: NPJ Genomic Medicine
#12
REVIEW
Kristen M Wigby, Deanna Brockman, Gregory Costain, Caitlin Hale, Stacie L Taylor, John Belmont, David Bick, David Dimmock, Susan Fernbach, John Greally, Vaidehi Jobanputra, Shashikant Kulkarni, Elizabeth Spiteri, Ryan J Taft
Early use of genome sequencing (GS) in the diagnostic odyssey can reduce suffering and improve care, but questions remain about which patient populations are most amenable to GS as a first-line diagnostic test. To address this, the Medical Genome Initiative conducted a literature review to identify appropriate clinical indications for GS. Studies published from January 2011 to August 2022 that reported on the diagnostic yield (DY) or clinical utility of GS were included. An exploratory meta-analysis using a random effects model evaluated DY based on cohort size and diagnosed cases per cohort...
February 26, 2024: NPJ Genomic Medicine
#13
JOURNAL ARTICLE
Ariel Dadush, Rona Merdler-Rabinowicz, David Gorelik, Ariel Feiglin, Ilana Buchumenski, Lipika R Pal, Shay Ben-Aroya, Eytan Ruppin, Erez Y Levanon
The majority of human genetic diseases are caused by single nucleotide variants (SNVs) in the genome sequence. Excitingly, new genomic techniques known as base editing have opened efficient pathways to correct erroneous nucleotides. Due to reliance on deaminases, which have the capability to convert A to I(G) and C to U, the direct applicability of base editing might seem constrained in terms of the range of mutations that can be reverted. In this evaluation, we assess the potential of DNA and RNA base editing methods for treating human genetic diseases...
February 26, 2024: NPJ Genomic Medicine
#14
JOURNAL ARTICLE
Debanjan Saha, Ha X Dang, Meng Zhang, David A Quigley, Felix Y Feng, Christopher A Maher
Metastatic castration-resistant prostate cancer (mCRPC) is a lethal form of prostate cancer. Although long-noncoding RNAs (lncRNAs) have been implicated in mCRPC, past studies have relied on bulk sequencing methods with low depth and lack of single-cell resolution. Hence, we performed a lncRNA-focused analysis of single-cell RNA-sequencing data (n = 14) from mCRPC biopsies followed by integration with bulk multi-omic datasets. This yielded 389 cell-enriched lncRNAs in prostate cancer cells and the tumor microenvironment (TME)...
February 23, 2024: NPJ Genomic Medicine
#15
JOURNAL ARTICLE
April Kennedy, Gabriel Ma, Roozbeh Manshaei, Rebekah K Jobling, Raymond H Kim, Tamorah Lewis, Iris Cohn
Commercial pharmacogenetic testing panels capture a fraction of the genetic variation underlying medication metabolism and predisposition to adverse reactions. In this study we compared variation in six pharmacogenes detected by whole genome sequencing (WGS) to a targeted commercial panel in a cohort of 308 individuals with family history of pediatric heart disease. In 1% of the cohort, WGS identified rare variants that altered the interpretation of metabolizer status and would thus prevent potential errors in gene-based dosing...
February 22, 2024: NPJ Genomic Medicine
#16
JOURNAL ARTICLE
Ayda Abolhassani, Zohreh Fattahi, Maryam Beheshtian, Mahsa Fadaee, Raheleh Vazehan, Fatemeh Ahangari, Shima Dehdahsi, Mehrshid Faraji Zonooz, Elham Parsimehr, Zahra Kalhor, Fatemeh Peymani, Maryam Mozaffarpour Nouri, Mojgan Babanejad, Khadijeh Noudehi, Fatemeh Fatehi, Shima Zamanian Najafabadi, Fariba Afroozan, Hilda Yazdan, Bita Bozorgmehr, Azita Azarkeivan, Shokouh Sadat Mahdavi, Pooneh Nikuei, Farzad Fatehi, Payman Jamali, Mahmoud Reza Ashrafi, Parvaneh Karimzadeh, Haleh Habibi, Kimia Kahrizi, Shahriar Nafissi, Ariana Kariminejad, Hossein Najmabadi
Next-generation sequencing (NGS) has been proven to be one of the most powerful diagnostic tools for rare Mendelian disorders. Several studies on the clinical application of NGS in unselected cohorts of Middle Eastern patients have reported a high diagnostic yield of up to 48%, correlated with a high level of consanguinity in these populations. We evaluated the diagnostic utility of NGS-based testing across different clinical indications in 1436 patients from Iran, representing the first study of its kind in this highly consanguineous population...
February 19, 2024: NPJ Genomic Medicine
#17
JOURNAL ARTICLE
Wataru Nakamura, Makoto Hirata, Satoyo Oda, Kenichi Chiba, Ai Okada, Raúl Nicolás Mateos, Masahiro Sugawa, Naoko Iida, Mineko Ushiama, Noriko Tanabe, Hiromi Sakamoto, Shigeki Sekine, Akira Hirasawa, Yosuke Kawai, Katsushi Tokunaga, Shin-Ichi Tsujimoto, Norio Shiba, Shuichi Ito, Teruhiko Yoshida, Yuichi Shiraishi
Innovations in sequencing technology have led to the discovery of novel mutations that cause inherited diseases. However, many patients with suspected genetic diseases remain undiagnosed. Long-read sequencing technologies are expected to significantly improve the diagnostic rate by overcoming the limitations of short-read sequencing. In addition, Oxford Nanopore Technologies (ONT) offers adaptive sampling and computationally driven target enrichment technology. This enables more affordable intensive analysis of target gene regions compared to standard non-selective long-read sequencing...
February 17, 2024: NPJ Genomic Medicine
#18
JOURNAL ARTICLE
Ilias Goranitis, Yan Meng, Melissa Martyn, Stephanie Best, Sophie Bouffler, Yvonne Bombard, Clara Gaff, Zornitza Stark
Health economic evidence is needed to inform the design of high-value and cost-effective processes for returning genomic results from analyses for additional findings (AF). This study reports the results of a discrete-choice experiment designed to elicit preferences for the process of returning AF results from the perspective of parents of children with rare conditions and to estimate the value placed on AF analysis. Overall, 94 parents recruited within the Australian Genomics and Melbourne Genomics programmes participated in the survey, providing preferences in a total of 1128 choice scenarios...
February 14, 2024: NPJ Genomic Medicine
#19
JOURNAL ARTICLE
Chalermkiat Kansuttiviwat, Pongtawat Lertwilaiwittaya, Ekkapong Roothumnong, Panee Nakthong, Peerawat Dungort, Chutima Meesamarnpong, Warisara Tansa-Nga, Khontawan Pongsuktavorn, Supakit Wiboonthanasarn, Warunya Tititumjariya, Nannipa Phuphuripan, Chittapat Lertbussarakam, Jantanee Wattanarangsan, Jiraporn Sritun, Kittiporn Punuch, Jirayu Kammarabutr, Pornthira Mutirangura, Wanna Thongnoppakhun, Chanin Limwongse, Manop Pithukpakorn
Multi-gene panel testing has led to the detection of pathogenic/likely pathogenic (P/LP) variants in many cancer susceptibility genes in patients with breast-ovarian cancer spectrum. However, the clinical and genomic data of Asian populations, including Thai cancer patients, was underrepresented, and the clinical significance of multi-gene panel testing in Thailand remains undetermined. In this study, we collected the clinical and genetic data from 4567 Thai patients with cancer in the hereditary breast-ovarian cancer (HBOC) spectrum who underwent multi-gene panel testing...
February 14, 2024: NPJ Genomic Medicine
#20
JOURNAL ARTICLE
Claude Bhérer, Robert Eveleigh, Katerina Trajanoska, Janick St-Cyr, Antoine Paccard, Praveen Nadukkalam Ravindran, Elizabeth Caron, Nimara Bader Asbah, Peyton McClelland, Clare Wei, Iris Baumgartner, Marc Schindewolf, Yvonne Döring, Danielle Perley, François Lefebvre, Pierre Lepage, Mathieu Bourgey, Guillaume Bourque, Jiannis Ragoussis, Vincent Mooser, Daniel Taliun
Whole genome sequencing (WGS) at high-depth (30X) allows the accurate discovery of variants in the coding and non-coding DNA regions and helps elucidate the genetic underpinnings of human health and diseases. Yet, due to the prohibitive cost of high-depth WGS, most large-scale genetic association studies use genotyping arrays or high-depth whole exome sequencing (WES). Here we propose a cost-effective method which we call "Whole Exome Genome Sequencing" (WEGS), that combines low-depth WGS and high-depth WES with up to 8 samples pooled and sequenced simultaneously (multiplexed)...
February 7, 2024: NPJ Genomic Medicine
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