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CCAFE: Estimating case and control allele frequencies from GWAS summary statistics. CCAFE:从GWAS汇总统计估计病例和对照等位基因频率。
IF 3.1
HGG Advances Pub Date : 2026-07-09 Epub Date: 2026-04-20 DOI: 10.1016/j.xhgg.2026.100616
Hayley R Stoneman, Hugo Lemus Gomez, Adelle Price, Christopher R Gignoux, Audrey E Hendricks
{"title":"CCAFE: Estimating case and control allele frequencies from GWAS summary statistics.","authors":"Hayley R Stoneman, Hugo Lemus Gomez, Adelle Price, Christopher R Gignoux, Audrey E Hendricks","doi":"10.1016/j.xhgg.2026.100616","DOIUrl":"10.1016/j.xhgg.2026.100616","url":null,"abstract":"<p><p>Genetic summary statistics can be used in a variety of analyses, such as causal inference, genetic correlation, and risk scores, to provide insights into the genetic architecture of conditions and traits. However, complete statistics are often not reported, limiting the utility of these data. Indeed, many post hoc analyses of diseases require case and control allele frequencies (AFs), which are not always published. Here, we present methods and software to derive case and control AFs from genome-wide association study (GWAS) summary statistics using the odds ratio, case and control sample sizes, and either the total (case and control aggregated) AF or the standard error (SE). In simulations and real data, derivations of case and control AFs using total AFs are highly accurate, whereas using SE underestimates AFs when covariates were included in the GWAS. While estimating case and control AFs using the total AF is preferred due to its high accuracy, the SE is more commonly available. Thus, we developed a bias adjustment using gnomAD AFs as a proxy for true AFs, reducing bias when using the SE. The methods and software provided here expand the utility of publicly available genetic summary statistics and promote the reusability of genomic data. The R package Case-Control Allele Frequency Estimation (CCAFE) is freely available on Bioconductor and GitHub.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100616"},"PeriodicalIF":3.1,"publicationDate":"2026-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13347939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147783541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Integrated transcriptomic and functional analysis reveals tissue-specific molecular pathology in adolescent idiopathic scoliosis. 综合转录组学和功能分析揭示了青少年特发性脊柱侧凸的组织特异性分子病理学。
IF 3.1
HGG Advances Pub Date : 2026-07-09 Epub Date: 2026-06-04 DOI: 10.1016/j.xhgg.2026.100631
Darius Ramkhalawan, Paola Parrales, Justin Koesterich, Gloria Montoya-Vazquez, Carlos Cuna, Anat Kreimer, Jessica McQuerry, Stephanie Ihnow, Nadja Makki
{"title":"Integrated transcriptomic and functional analysis reveals tissue-specific molecular pathology in adolescent idiopathic scoliosis.","authors":"Darius Ramkhalawan, Paola Parrales, Justin Koesterich, Gloria Montoya-Vazquez, Carlos Cuna, Anat Kreimer, Jessica McQuerry, Stephanie Ihnow, Nadja Makki","doi":"10.1016/j.xhgg.2026.100631","DOIUrl":"10.1016/j.xhgg.2026.100631","url":null,"abstract":"<p><p>Adolescent idiopathic scoliosis (AIS), the spontaneous development of a lateral spine curvature during puberty, is the most common pediatric spine disorder, affecting ∼3% of children worldwide. As the underlying etiology remains unclear, AIS is treated purely symptomatically, initially by bracing and ultimately by highly invasive, costly surgeries. Genome-wide association studies (GWASs) have identified numerous risk loci in non-coding genomic regions, making it difficult to link them to a biological function. To address this, we performed a multi-tissue investigation to connect genetic risk to tissue-specific molecular pathology. We conducted RNA sequencing on the primary tissues implicated in AIS, paraspinal muscle and spinal cartilage, from patients and unaffected control subjects. In paraspinal muscle, we identified differentially expressed genes (DEGs) enriched for pathways related to muscle structure, myogenesis, and metabolism. Key upregulated genes include the transcription factor EGR1 and structural components, such as MYH1. In spinal cartilage, we found enrichment of genes related to TGFβ and FoxO signaling, as well as metabolic pathways. Notably, genes crucial for chondrocyte differentiation (e.g., SOX5 and SOX6) were significantly downregulated. We then examined genes at known GWAS loci and found that several risk-associated genes were differentially expressed in one or both tissues. To investigate the function of non-coding variants at these loci, we identified and validated several enhancer elements harboring AIS risk SNPs at the BCL2, ADGRG6, BNC2, and FTO loci. We reveal distinct pathological signatures in muscle and cartilage and lay the foundation for connecting non-coding genetic risk to the dysregulation of key developmental and structural pathways.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100631"},"PeriodicalIF":3.1,"publicationDate":"2026-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13316586/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148164880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Positive selection on brain cis-regulatory elements in the human lineage drives changes in gene expression and susceptibility to neuropsychiatric disorders. 人类谱系中脑顺式调控元件的正向选择驱动基因表达差异和对神经精神疾病的易感性。
IF 3.1
HGG Advances Pub Date : 2026-07-09 Epub Date: 2026-05-21 DOI: 10.1016/j.xhgg.2026.100629
Youness Touissi, Eric J Vallender
{"title":"Positive selection on brain cis-regulatory elements in the human lineage drives changes in gene expression and susceptibility to neuropsychiatric disorders.","authors":"Youness Touissi, Eric J Vallender","doi":"10.1016/j.xhgg.2026.100629","DOIUrl":"10.1016/j.xhgg.2026.100629","url":null,"abstract":"<p><p>Human brain evolution is hypothesized to be driven primarily by regulatory rather than protein-coding changes. Identifying evolutionary changes in regulatory elements, however, has been constrained by numbers and relationships of taxa and by methodology targeting conserved sequences. These approaches are independent of any experimental assessment of function and overlook potential neofunctionalization in less constrained regions. Here, we leveraged 243 primate genomes to apply a human branch-specific positive selection test to over 350,000 experimentally confirmed human brain-active cis-regulatory elements, identifying 8,522 elements under positive selection on the human lineage. Genes regulated by human positively selected elements showed differential expression between humans and macaques during fetal and adult stages compared to non-selected elements. Elements under positive selection that remained active across fetal and adult stages showed the strongest enrichment for genetic variants associated with neuropsychiatric conditions, including schizophrenia and bipolar disorder.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100629"},"PeriodicalIF":3.1,"publicationDate":"2026-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13266179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147989430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A homozygous nonsense variant in the oligosaccharyltransferase complex gene, RPN1, causes a congenital disorder of glycosylation. 低聚糖转移酶复合体基因RPN1的纯合无义变异导致先天性糖基化障碍。
IF 3.1
HGG Advances Pub Date : 2026-07-09 Epub Date: 2026-04-03 DOI: 10.1016/j.xhgg.2026.100604
Bobby G Ng, Wenyue Zhang, Jennifer E Neil, Marwa Danish, Dana Marafi, Tarek M Kamal, Laila Bastaki, Muna Al Saffar, Edward Yang, Miao He, Christopher A Walsh, Ganeshwaran H Mochida, Hudson H Freeze
{"title":"A homozygous nonsense variant in the oligosaccharyltransferase complex gene, RPN1, causes a congenital disorder of glycosylation.","authors":"Bobby G Ng, Wenyue Zhang, Jennifer E Neil, Marwa Danish, Dana Marafi, Tarek M Kamal, Laila Bastaki, Muna Al Saffar, Edward Yang, Miao He, Christopher A Walsh, Ganeshwaran H Mochida, Hudson H Freeze","doi":"10.1016/j.xhgg.2026.100604","DOIUrl":"10.1016/j.xhgg.2026.100604","url":null,"abstract":"<p><p>Congenital disorders of glycosylation (CDGs) are a phenotypically diverse group of genetic conditions arising from pathogenic variants in various glycosylation pathways. The most prevalent are N-glycosylation disorders. Here, we present clinical and biochemical data on two siblings with a neurodevelopmental disorder and a pathogenic homozygous nonsense variant in ribophorin I (RPN1), an essential component of the oligosaccharyltransferase (OST) complex. Both affected individuals showed a classical type I serum transferrin profile, while lymphoblasts revealed that the variant resulted in a truncated RPN1 protein with reduced levels. The protein stability of other essential OST complex components, including STT3 OST complex catalytic subunit A (STT3A), RPN2, and dolichyl-diphosphooligosaccharide (DDOST), was also significantly reduced. Structural modeling of both OST-A and OST-B complexes shows that RPN1 truncation eliminates a C-terminal four-helix bundle, which interacts with the translating ribosome. This interaction is necessary and specific for the co-translational activity of the OST-A complex. Supporting this observation, hypoglycosylation of an OST-A-specific substrate protein was observed, while OST-B-specific substrates were unaffected. These data convey that a rare loss-of-function RPN1 variant causes an autosomal recessive CDG characterized by neurodevelopmental deficits.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100604"},"PeriodicalIF":3.1,"publicationDate":"2026-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13112475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147623808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A framework for the molecular identification of CHIP for clinical research. 用于临床研究的CHIP分子鉴定框架。
IF 3.1
HGG Advances Pub Date : 2026-04-09 Epub Date: 2026-01-20 DOI: 10.1016/j.xhgg.2026.100575
Philip Harraka, Robert L O'Reilly, Jared Burke, Paul Yeh, Kerryn Howlett, Kiarash Behrouzfar, Daniele Belluoccio, Amanda Rewse, Brigid M Lynch, Kristen J Bubb, Stephen J Nicholls, Roger L Milne, Melissa C Southey
{"title":"A framework for the molecular identification of CHIP for clinical research.","authors":"Philip Harraka, Robert L O'Reilly, Jared Burke, Paul Yeh, Kerryn Howlett, Kiarash Behrouzfar, Daniele Belluoccio, Amanda Rewse, Brigid M Lynch, Kristen J Bubb, Stephen J Nicholls, Roger L Milne, Melissa C Southey","doi":"10.1016/j.xhgg.2026.100575","DOIUrl":"10.1016/j.xhgg.2026.100575","url":null,"abstract":"<p><p>Clonal hematopoiesis of indeterminate potential (CHIP) is associated with many diseases of aging. Large research initiatives are needed to develop clinical guidelines for the management of individuals with CHIP and their risk of disease. However, little guidance is available for the classification of variants as CHIP associated or how to identify individuals consistently and systematically as having CHIP. This study aimed to develop and execute a resource-mindful framework for identifying individuals with CHIP, and those without, for downstream clinical studies. This framework was used to categorize CHIP in a cross-section of 2,328 participants from the Australian Breakthrough Cancer Study. DNA extracted from saliva samples was sequenced for a panel of ten gene regions that frequently carry variants that are associated with CHIP. Variants in these regions were curated for CHIP according to field-specific criteria. Individuals were categorized as either CHIP positive, CHIP negative, or CHIP indeterminate based on their variant findings. Sequencing was successfully performed on 2,328 individuals. The mean age (± standard deviation) was 68 ± 3 years, and 48% were men. 347 participants (15%) were identified as CHIP positive with a total of 400 CHIP-associated variants. 1,442 participants (62%) were considered CHIP negative based on finding no somatic variation within the target regions. The remaining 539 (23%) were considered CHIP indeterminate because they had at least one variant that could not be interpreted. This framework provides a consistent approach to the categorization of individuals as CHIP positive or CHIP negative for clinical research and provides an opportunity for improved harmonization in the curation of CHIP.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100575"},"PeriodicalIF":3.1,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12925157/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146019865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ASAH2 deficiency affects sphingolipid homeostasis and neuromotor control, causing a progressive neurological disorder. ASAH2缺乏影响鞘脂稳态和神经运动控制,导致进行性神经系统疾病。
IF 3.1
HGG Advances Pub Date : 2026-04-09 Epub Date: 2026-03-10 DOI: 10.1016/j.xhgg.2026.100587
Marcello Scala, Ranjan K Sahu, Mariasavina Severino, Monica Traverso, Michele Iacomino, Marina Pedemonte, Filippo Santorelli, Stefano Tozza, Federico Zara, Chiara Fiorillo, Hyung-Lok Chung
{"title":"ASAH2 deficiency affects sphingolipid homeostasis and neuromotor control, causing a progressive neurological disorder.","authors":"Marcello Scala, Ranjan K Sahu, Mariasavina Severino, Monica Traverso, Michele Iacomino, Marina Pedemonte, Filippo Santorelli, Stefano Tozza, Federico Zara, Chiara Fiorillo, Hyung-Lok Chung","doi":"10.1016/j.xhgg.2026.100587","DOIUrl":"10.1016/j.xhgg.2026.100587","url":null,"abstract":"<p><p>Sphingolipids are integral components of cell membranes and modulate cell survival, proliferation, and apoptosis. ASAH2 is a brain- and gut-enriched gene encoding the neutral N-acylsphingosine amidohydrolase 2, a poorly characterized member of the human ceramidase family. This enzyme plays a pivotal role in maintaining the sphingolipid homeostasis, which is crucial for neurogenesis and synaptic function in the central and peripheral nervous systems. In fact, a dysregulated sphingolipid metabolism is associated with progressive neurological conditions, including Alzheimer disease and Parkinson disease. Here, we report the identification of biallelic ASAH2 variants in an individual with a neurodevelopmental condition featuring cognitive impairment, neuropathy, ophthalmoplegia, and progressive cerebellar and extraocular muscles atrophy. Through exome sequencing, we identified very rare missense ASAH2 variants, predicted to be deleterious by in silico analyses. Muscle biopsy histopathologic evaluation revealed features suggestive of neuropathic damage. Lipidomic profiling revealed a hyper-accumulation of glucosylceramide in the subject's cells. Then, the functional investigation of the ASAH2 variants in Drosophila showed the production of an unstable protein and consistent loss-of-function neuromotor phenotypes. Our findings support ASAH2 as a candidate gene for a previously uncharacterized neurodevelopmental disorder with neuropathic features and progressive cerebellar atrophy, underscoring the important role of this ceramidase in human nervous systems.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100587"},"PeriodicalIF":3.1,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13022665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147436301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Patient-informed CRISPR screen identifies FLNB as a congenital heart disease and ciliopathy gene. 患者知情的CRISPR筛选确定FLNB为先天性心脏病和纤毛病基因
IF 3.1
HGG Advances Pub Date : 2026-04-09 Epub Date: 2026-02-10 DOI: 10.1016/j.xhgg.2026.100580
Angelo Arrigo, Venkatramanan Rao, Aakrosh Ratan, Saurabh S Kulkarni
{"title":"Patient-informed CRISPR screen identifies FLNB as a congenital heart disease and ciliopathy gene.","authors":"Angelo Arrigo, Venkatramanan Rao, Aakrosh Ratan, Saurabh S Kulkarni","doi":"10.1016/j.xhgg.2026.100580","DOIUrl":"10.1016/j.xhgg.2026.100580","url":null,"abstract":"<p><p>Heterotaxy (HTX) is a congenital disorder characterized by abnormal left-right organ placement, often leading to severe congenital heart disease (CHD). Despite advances in sequencing, many CHD and HTX-associated genes remain functionally unvalidated, hindering effective clinical diagnosis and management. Here, we leveraged a high-throughput CRISPR-Cas9 screening approach in the Xenopus model to rapidly evaluate candidate genes identified from whole-exome sequencing of human CHD patients. Our screen identified Filamin B (FLNB), an actin-binding protein previously linked to skeletal disorders but not to ciliopathies or CHD. We identified 5 probands with CHD and HTX, 3 with recessive and 2 with damaging heterozygous variants in FLNB. Disrupting flnb in Xenopus reproduced key features of the human HTX phenotype, including defects in cardiac development and impaired motile cilia function. Rescue experiments confirmed the functional conservation of human FLNB, directly implicating actin cytoskeletal disruption in ciliogenesis and left-right patterning defects. Our results provide crucial evidence linking human FLNB dysfunction to ciliopathies and CHD and HTX.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100580"},"PeriodicalIF":3.1,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12974105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146167070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
EEFSEC deficiency underlies a human selenopathy with primary neurodevelopmental origins via midbrain-hindbrain hypoplasia. EEFSEC缺乏是由中脑-后脑发育不全引起的原发性神经发育起源的人硒病的基础。
IF 3.1
HGG Advances Pub Date : 2026-04-09 Epub Date: 2026-01-09 DOI: 10.1016/j.xhgg.2026.100563
Zhiyi Xia, Hui Liu, Pengbo Guo, Chongfen Chen, Lili Ge, Longfei Tang, Yaodong Zhang, Yanli Ma
{"title":"EEFSEC deficiency underlies a human selenopathy with primary neurodevelopmental origins via midbrain-hindbrain hypoplasia.","authors":"Zhiyi Xia, Hui Liu, Pengbo Guo, Chongfen Chen, Lili Ge, Longfei Tang, Yaodong Zhang, Yanli Ma","doi":"10.1016/j.xhgg.2026.100563","DOIUrl":"10.1016/j.xhgg.2026.100563","url":null,"abstract":"<p><p>Bi-allelic mutations in EEFSEC, a key factor in selenoprotein synthesis, cause a severe human selenopathy characterized by developmental delay, spasticity, and profound cerebellar atrophy. While previous studies in invertebrate models framed this condition as an early-onset neurodegenerative disorder, the contribution of primary developmental defects to the severe brain malformations in patients has remained a critical unanswered question. Here, we address this gap using a zebrafish model of EEFSEC deficiency. We discovered that loss of eefsec function does not impair global somatic growth but instead causes specific and significant hypoplasia of the midbrain and hindbrain-the embryonic precursors to the human cerebellum and brain stem. These structural defects directly correlate with robust behavioral impairments, including diminished locomotion and blunted escape responses, mirroring the severe motor dysfunction in patients. Critically, our findings provide the in vivo evidence from a vertebrate model that this disorder involves a primary neurodevelopmental defect, which underlies the severe brain malformations and creates a structurally vulnerable nervous system. This establishes a developmental basis for understanding this condition. We propose that this initial failure in brain construction, which we term a developmental selenopathy, creates a structurally vulnerable nervous system, providing a plausible mechanistic explanation for the human phenotype and proposing a framework for understanding this devastating condition.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100563"},"PeriodicalIF":3.1,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12861234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145946054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Scaling genomic reanalysis to unlock diagnoses and transform rare disease care. 扩大基因组再分析解锁诊断和转变罕见病护理。
IF 3.1
HGG Advances Pub Date : 2026-04-09 Epub Date: 2026-02-18 DOI: 10.1016/j.xhgg.2026.100582
Shira Rockowitz, Wanqing Shao, Courtney French, Tina K Truong, Jacob Hagen, Rylee McGonigle, Alexa Geltzeiler, Beth Sheidley, Lacey Smith, Alissa M D'Gama, Mira Irons, Janet Chou, Joan Stoler, Amy Kritzer, Lance Rodan, Akiko Shimamura, Olaf Bodamer, Stephanie Sacharow, Janet S Soul, Siddharth Srivastava, Amy Roberts Kennedy, Aya Abu-El-Haija, Abbe Lai, Heather Olson, Jane Juusola, Erin Ryan, Bethany Friedman, Anupama Singh, Cliff Li, Rittika Mallik, Gwendolyn Strickland, Gillian Prinzing, Alisa Mo, Anne O'Donnell-Luria, Jeff Bolton, Philip M Boone, William Brucker, Michael Duyzend, Sonal Mahida, David T Miller, Jacklyn Omorodion, Jeanette Petit, Jonathan Picker, Annapurna Poduri, Colleen Carlston, Monica H Wojcik, Piotr Sliz, Wendy K Chung
{"title":"Scaling genomic reanalysis to unlock diagnoses and transform rare disease care.","authors":"Shira Rockowitz, Wanqing Shao, Courtney French, Tina K Truong, Jacob Hagen, Rylee McGonigle, Alexa Geltzeiler, Beth Sheidley, Lacey Smith, Alissa M D'Gama, Mira Irons, Janet Chou, Joan Stoler, Amy Kritzer, Lance Rodan, Akiko Shimamura, Olaf Bodamer, Stephanie Sacharow, Janet S Soul, Siddharth Srivastava, Amy Roberts Kennedy, Aya Abu-El-Haija, Abbe Lai, Heather Olson, Jane Juusola, Erin Ryan, Bethany Friedman, Anupama Singh, Cliff Li, Rittika Mallik, Gwendolyn Strickland, Gillian Prinzing, Alisa Mo, Anne O'Donnell-Luria, Jeff Bolton, Philip M Boone, William Brucker, Michael Duyzend, Sonal Mahida, David T Miller, Jacklyn Omorodion, Jeanette Petit, Jonathan Picker, Annapurna Poduri, Colleen Carlston, Monica H Wojcik, Piotr Sliz, Wendy K Chung","doi":"10.1016/j.xhgg.2026.100582","DOIUrl":"10.1016/j.xhgg.2026.100582","url":null,"abstract":"<p><p>Genomic reanalysis can identify causative variants for rare diseases as patient phenotypes evolve and gene-disease knowledge expands. Despite its diagnostic value, routine reanalysis is limited by clinician capacity, lack of patient follow-up, data silos, cost, and lack of availability of clinical data to testing laboratories that are not obligated to conduct reanalysis. The Children's Rare Disease Collaborative at Boston Children's Hospital (BCH) has integrated genomic and phenotypic data from over 15,500 patients into a clinician-facing platform. Leveraging this infrastructure, we developed a Proactive Genomic Reanalysis (PGR) workflow at BCH for clinical sequencing data that is centralized, semi-automated, and clinically integrated. Here, we report initial results and outline required resources and transferable insights applicable to other healthcare settings. Initial pilot implementation, applied to a subset of clinical sequencing patients' data, revealed practical challenges, notably clinician turnover and patient recontact difficulties. Of 42 patients' candidate variants discovered by the PGR bioinformatics pipeline and returned to treating clinicians, 33 were determined to have a high suspicion of disease causality and an additional 3 were determined to be candidate variant of uncertain significance. A process to generate reports and return results to patients was initiated when applicable. Although the initial pilot implementation was limited, the PGR bioinformatics pipeline is designed to be utilized iteratively, making reanalysis a continuing process. This work highlights the feasibility and impact of centralized PGR processes and the potential for healthcare institutions to scale genomic reanalysis.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100582"},"PeriodicalIF":3.1,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12993396/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146228930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of alternative splicing in WFS1 associated with low-frequency hearing loss in the common marmoset. 与普通狨猴低频听力损失相关的WFS1选择性剪接的鉴定
IF 3.1
HGG Advances Pub Date : 2026-04-09 Epub Date: 2026-02-07 DOI: 10.1016/j.xhgg.2026.100578
Shu Yokota, Hidekane Yoshimura, Shin-Ya Nishio, Erika Sasaki, Keisuke Mukasa, Shin-Ichi Usami, Yutaka Takumi
{"title":"Identification of alternative splicing in WFS1 associated with low-frequency hearing loss in the common marmoset.","authors":"Shu Yokota, Hidekane Yoshimura, Shin-Ya Nishio, Erika Sasaki, Keisuke Mukasa, Shin-Ichi Usami, Yutaka Takumi","doi":"10.1016/j.xhgg.2026.100578","DOIUrl":"10.1016/j.xhgg.2026.100578","url":null,"abstract":"<p><p>Approximately 200 genes have been identified as causative in hereditary hearing loss. Genetic testing is increasingly important, not only for accurate diagnosis but also for predicting audiometric profiles, prognoses, and potential syndromic features. Hereditary hearing loss can be syndromic or nonsyndromic, with nonsyndromic forms further classified by inheritance: autosomal-dominant or autosomal-recessive. In autosomal-dominant cases, three pathological mechanisms-haploinsufficiency, dominant-negative effects, and gain of function-are often implicated. Moreover, specific genes correlate with distinct audiometric patterns: WFS1 variants typically cause low-frequency hearing loss, whereas KCNQ4 and POU4F3 variants are linked to high-frequency loss. To investigate the underlying mechanisms of these frequency-dependent patterns, gene expression across cochlear turns was compared in mice, but interpretations of the results were limited because of inherent structural differences between rodent and primate cochleae. Therefore, the common marmoset (Callithrix jacchus), which offers closer anatomical and functional similarity to human cochleae, was utilized herein as an improved model. Using RNA sequencing (RNA-seq) across cochlear turns of common marmosets, the present study aimed to uncover gene expression and alternative splicing patterns that may explain tonotopic manifestations in hereditary hearing loss, including those caused by WFS1 variants, the present study being one such using common marmoset cochlear RNA-seq data, and these findings are highly valuable for genetic diagnosis and the development of gene therapies.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100578"},"PeriodicalIF":3.1,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12936726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146137916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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