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person:evrong01
Chemotherapy and the somatic mutation burden of sperm
Picciotto, Shany; Arenas-Gallo, Camilo; Toren, Amos; Mehrian-Shai, Ruty; Daly, Bryan; Rhodes, Stephen; Prunty, Megan; Liu, Ruolin; Bohorquez, Anyull; Grońska-Pęski, Marta; Melanaphy, Shana; Callum, Pamela; Lassen, Emilie; Skytte, Anne-Bine; Obeng, Rebecca C; Barbieri, Christopher; Gallogly, Molly; Cooper, Brenda; Daunov, Katherine; Beard, Lydia; Van-Besien, Koen; Halpern, Joshua; Pan, Quintin; Evrony, Gilad D; Adalsteinsson, Viktor A; Shoag, Jonathan E
Many chemotherapeutic agents impair cancer growth by inducing DNA damage. The impact of these agents on mutagenesis in normal cells, including sperm, is largely unknown. Here, we applied high-fidelity duplex sequencing to 94 samples from 36 individuals exposed to diverse chemotherapies and 32 controls. We found that many of the sperm samples from men exposed to chemotherapy, the mutation burden was elevated as compared to controls and the expected burden based on trio studies, with one subject having >10-fold increase over expected for age. Saliva from this same individual also had a markedly higher mutation burden. We then validated this finding using other tissues, also finding an increased mutation burden in the blood and liver of many subjects exposed to chemotherapy as compared to unexposed controls. Similarly, mice treated with three cycles of cisplatin had an increased mutation burden in sperm but also in the liver, and hematopoietic progenitor cells. These results suggest an association between cancer therapies and mutation burden, with implications for counseling cancer patients considering banking sperm prior to therapy and for cancer survivors considering the tradeoffs of using banked sperm as compared to conceiving naturally.
PMID: 40359030
ISSN: 2379-3708
CID: 5844152
Deficiency of the Fanconi anemia core complex protein FAAP100 results in severe Fanconi anemia
Harrison, Benjamin A; Mizrahi-Powell, Emma; Pappas, John; Thomas, Kristen; Vasishta, Subrahmanya; Hebbar, Shripad; Shukla, Anju; Nayak, Shalini S; Truong, Tina K; Woroch, Amy; Kharbutli, Yara; Gelb, Bruce D; Mintz, Cassie S; Evrony, Gilad D; Smogorzewska, Agata
Fanconi anemia (FA) is a rare genetic disease characterized by loss-of-function variants in any of the 22 previously identified genes (FANCA-FANCW) that encode proteins participating in the repair of DNA interstrand crosslinks (ICLs). Patient phenotypes are variable, but may include developmental abnormalities, early onset pancytopenia, and predisposition to hematologic and solid tumors. Here, we describe two unrelated families with multiple pregnancy losses and offspring presenting with severe developmental and hematologic abnormalities leading to death in utero or in early life. Homozygous loss-of-function variants in FAAP100 were identified in affected children of both families. The FAAP100 protein associates with FANCB and FANCL, the E3 ubiquitin ligase responsible for the monoubiquitination of FANCD2 and FANCI, which is necessary for FA pathway function. Patient-derived cells exhibited phenotypes consistent with FA. Expression of the wild-type FAAP100 cDNA, but not the patient-derived variants, rescued the observed cellular phenotypes. This establishes FAAP100 deficiency as a cause of Fanconi anemia, with FAAP100 gaining an alias as FANCX. The extensive developmental malformations of individuals with FAAP100 loss-of-function variants are among the most severe across previously described FA phenotypes, indicating that the FA pathway is essential for human development.
PMID: 40244696
ISSN: 1558-8238
CID: 5828682
Direct measurement of the male germline mutation rate in individuals using sequential sperm samples
Shoag, Jonathan E; Srinivasa, Amoolya; Loh, Caitlin A; Liu, Mei Hong; Lassen, Emilie; Melanaphy, Shana; Costa, Benjamin M; Grońska-Pęski, Marta; Jabara, Nisrine T; Picciotto, Shany; Choi, Una; Bohorquez, Anyull D; Barbieri, Christopher E; Callum, Pamela; Skytte, Anne-Bine; Evrony, Gilad D
Mutations that accumulate in the human male germline with age are a major driver of genetic diversity and contribute to genetic diseases. However, aging-related male germline mutation rates have not been measured directly in germline cells (sperm) at the level of individuals. We developed a study design in which we recalled 23 sperm donors with prior banked samples to provide new sperm samples. The old and new sequential sperm samples were separated by long timespans, ranging from 10 to 33 years. We profiled these samples by high-fidelity duplex sequencing and demonstrate that direct high-fidelity sequencing of sperm yields cohort-wide mutation rates and patterns consistent with prior family-based (trio) studies. In every individual, we detected an increase in sperm mutation burden between the two sequential samples, yielding individual-specific measurements of germline mutation rate. Deep whole-genome sequencing of sequential sperm samples from two individuals followed by targeted validation measured remarkably stable mosaicism of clonal mutations that likely arose during embryonic and germline development, suggesting that age did not substantially impact the diversity of spermatogonial stem cell pools in these individuals. Our application of high-fidelity and deep whole-genome sequencing to sequential sperm samples provides insight into aging-related mutation processes in the male germline.
PMCID:11910575
PMID: 40089484
ISSN: 2041-1723
CID: 5812882
Ultra-rapid droplet digital PCR enables intraoperative tumor quantification
Murphy, Zachary R; Bianchini, Emilia C; Smith, Andrew; Körner, Lisa I; Russell, Teresa; Reinecke, David; Maarouf, Nader; Wang, Yuxiu; Golfinos, John G; Miller, Alexandra M; Snuderl, Matija; Orringer, Daniel A; Evrony, Gilad D
BACKGROUND:The diagnosis and treatment of tumors often depend on molecular-genetic data. However, rapid and iterative access to molecular data is not currently feasible during surgery, complicating intraoperative diagnosis and precluding measurement of tumor cell burdens at surgical margins to guide resections. METHODS:Here, we introduce Ultra-Rapid droplet digital PCR (UR-ddPCR), a technology that achieves the fastest measurement, to date, of mutation burdens in tissue samples, from tissue to result in 15 min. Our workflow substantially reduces the time from tissue biopsy to molecular diagnosis and provides a highly accurate means of quantifying residual tumor infiltration at surgical margins. FINDINGS/RESULTS: = 0.995). CONCLUSIONS:The technology and workflow developed here enable intraoperative molecular-genetic assays with unprecedented speed and sensitivity. We anticipate that our method will facilitate novel point-of-care diagnostics and molecularly guided surgeries that improve clinical outcomes. FUNDING/BACKGROUND:This study was funded by the National Institutes of Health and NYU Grossman School of Medicine institutional funds. Reagents and instruments were provided in kind by Bio-Rad.
PMID: 40010345
ISSN: 2666-6340
CID: 5801032
High-fidelity, large-scale targeted profiling of microsatellites
Loh, Caitlin A; Shields, Danielle A; Schwing, Adam; Evrony, Gilad D
Microsatellites are highly mutable sequences that can serve as markers for relationships among individuals or cells within a population. The accuracy and resolution of reconstructing these relationships depends on the fidelity of microsatellite profiling and the number of microsatellites profiled. However, current methods for targeted profiling of microsatellites incur significant "stutter" artifacts that interfere with accurate genotyping, and sequencing costs preclude whole-genome microsatellite profiling of a large number of samples. We developed a novel method for accurate and cost-effective targeted profiling of a panel of more than 150,000 microsatellites per sample, along with a computational tool for designing large-scale microsatellite panels. Our method addresses the greatest challenge for microsatellite profiling-"stutter" artifacts-with a low-temperature hybridization capture that significantly reduces these artifacts. We also developed a computational tool for accurate genotyping of the resulting microsatellite sequencing data that uses an ensemble approach integrating three microsatellite genotyping tools, which we optimize by analysis of de novo microsatellite mutations in human trios. Altogether, our suite of experimental and computational tools enables high-fidelity, large-scale profiling of microsatellites, which may find utility in diverse applications such as lineage tracing, population genetics, ecology, and forensics.
PMID: 39013593
ISSN: 1549-5469
CID: 5680192
DNA mismatch and damage patterns revealed by single-molecule sequencing
Liu, Mei Hong; Costa, Benjamin M; Bianchini, Emilia C; Choi, Una; Bandler, Rachel C; Lassen, Emilie; Grońska-Pęski, Marta; Schwing, Adam; Murphy, Zachary R; Rosenkjær, Daniel; Picciotto, Shany; Bianchi, Vanessa; Stengs, Lucie; Edwards, Melissa; Nunes, Nuno Miguel; Loh, Caitlin A; Truong, Tina K; Brand, Randall E; Pastinen, Tomi; Wagner, J Richard; Skytte, Anne-Bine; Tabori, Uri; Shoag, Jonathan E; Evrony, Gilad D
Mutations accumulate in the genome of every cell of the body throughout life, causing cancer and other diseases1,2. Most mutations begin as nucleotide mismatches or damage in one of the two strands of the DNA before becoming double-strand mutations if unrepaired or misrepaired3,4. However, current DNA-sequencing technologies cannot accurately resolve these initial single-strand events. Here we develop a single-molecule, long-read sequencing method (Hairpin Duplex Enhanced Fidelity sequencing (HiDEF-seq)) that achieves single-molecule fidelity for base substitutions when present in either one or both DNA strands. HiDEF-seq also detects cytosine deamination-a common type of DNA damage-with single-molecule fidelity. We profiled 134 samples from diverse tissues, including from individuals with cancer predisposition syndromes, and derive from them single-strand mismatch and damage signatures. We find correspondences between these single-strand signatures and known double-strand mutational signatures, which resolves the identity of the initiating lesions. Tumours deficient in both mismatch repair and replicative polymerase proofreading show distinct single-strand mismatch patterns compared to samples that are deficient in only polymerase proofreading. We also define a single-strand damage signature for APOBEC3A. In the mitochondrial genome, our findings support a mutagenic mechanism occurring primarily during replication. As double-strand DNA mutations are only the end point of the mutation process, our approach to detect the initiating single-strand events at single-molecule resolution will enable studies of how mutations arise in a variety of contexts, especially in cancer and ageing.
PMID: 38867045
ISSN: 1476-4687
CID: 5669192
Ultra-Rapid Droplet Digital PCR Enables Intraoperative Tumor Quantification
Murphy, Zachary R; Bianchini, Emilia C; Smith, Andrew; Körner, Lisa I; Russell, Teresa; Reinecke, David; Wang, Yuxiu; Snuderl, Matija; Orringer, Daniel A; Evrony, Gilad D
The diagnosis and treatment of tumors often depends on molecular-genetic data. However, rapid and iterative access to molecular data is not currently feasible during surgery, complicating intraoperative diagnosis and precluding measurement of tumor cell burdens at surgical margins to guide resections. To address this gap, we developed Ultra-Rapid droplet digital PCR (UR-ddPCR), which can be completed in 15 minutes from tissue to result with an accuracy comparable to standard ddPCR. We demonstrate UR-ddPCR assays for the IDH1 R132H and BRAF V600E clonal mutations that are present in many low-grade gliomas and melanomas, respectively. We illustrate the clinical feasibility of UR-ddPCR by performing it intraoperatively for 13 glioma cases. We further combine UR-ddPCR measurements with UR-stimulated Raman histology intraoperatively to estimate tumor cell densities in addition to tumor cell percentages. We anticipate that UR-ddPCR, along with future refinements in assay instrumentation, will enable novel point-of-care diagnostics and the development of molecularly-guided surgeries that improve clinical outcomes.
PMCID:11160868
PMID: 38854127
CID: 5668772
Pangenome graphs improve the analysis of structural variants in rare genetic diseases
Groza, Cristian; Schwendinger-Schreck, Carl; Cheung, Warren A; Farrow, Emily G; Thiffault, Isabelle; Lake, Juniper; Rizzo, William B; Evrony, Gilad; Curran, Tom; Bourque, Guillaume; Pastinen, Tomi
Rare DNA alterations that cause heritable diseases are only partially resolvable by clinical next-generation sequencing due to the difficulty of detecting structural variation (SV) in all genomic contexts. Long-read, high fidelity genome sequencing (HiFi-GS) detects SVs with increased sensitivity and enables assembling personal and graph genomes. We leverage standard reference genomes, public assemblies (n = 94) and a large collection of HiFi-GS data from a rare disease program (Genomic Answers for Kids, GA4K, n = 574 assemblies) to build a graph genome representing a unified SV callset in GA4K, identify common variation and prioritize SVs that are more likely to cause genetic disease (MAF < 0.01). Using graphs, we obtain a higher level of reproducibility than the standard reference approach. We observe over 200,000 SV alleles unique to GA4K, including nearly 1000 rare variants that impact coding sequence. With improved specificity for rare SVs, we isolate 30 candidate SVs in phenotypically prioritized genes, including known disease SVs. We isolate a novel diagnostic SV in KMT2E, demonstrating use of personal assemblies coupled with pangenome graphs for rare disease genomics. The community may interrogate our pangenome with additional assemblies to discover new SVs within the allele frequency spectrum relevant to genetic diseases.
PMCID:10803329
PMID: 38253606
ISSN: 2041-1723
CID: 5624712
Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort
Cheung, Warren A; Johnson, Adam F; Rowell, William J; Farrow, Emily; Hall, Richard; Cohen, Ana S A; Means, John C; Zion, Tricia N; Portik, Daniel M; Saunders, Christopher T; Koseva, Boryana; Bi, Chengpeng; Truong, Tina K; Schwendinger-Schreck, Carl; Yoo, Byunggil; Johnston, Jeffrey J; Gibson, Margaret; Evrony, Gilad; Rizzo, William B; Thiffault, Isabelle; Younger, Scott T; Curran, Tom; Wenger, Aaron M; Grundberg, Elin; Pastinen, Tomi
Long-read HiFi genome sequencing allows for accurate detection and direct phasing of single nucleotide variants, indels, and structural variants. Recent algorithmic development enables simultaneous detection of CpG methylation for analysis of regulatory element activity directly in HiFi reads. We present a comprehensive haplotype resolved 5-base HiFi genome sequencing dataset from a rare disease cohort of 276 samples in 152 families to identify rare (~0.5%) hypermethylation events. We find that 80% of these events are allele-specific and predicted to cause loss of regulatory element activity. We demonstrate heritability of extreme hypermethylation including rare cis variants associated with short (~200 bp) and large hypermethylation events (>1 kb), respectively. We identify repeat expansions in proximal promoters predicting allelic gene silencing via hypermethylation and demonstrate allelic transcriptional events downstream. On average 30-40 rare hypermethylation tiles overlap rare disease genes per patient, providing indications for variation prioritization including a previously undiagnosed pathogenic allele in DIP2B causing global developmental delay. We propose that use of HiFi genome sequencing in unsolved rare disease cases will allow detection of unconventional diseases alleles due to loss of regulatory element activity.
PMCID:10226990
PMID: 37248219
ISSN: 2041-1723
CID: 5541202
Single duplex DNA sequencing with CODEC detects mutations with high sensitivity
Bae, Jin H; Liu, Ruolin; Roberts, Eugenia; Nguyen, Erica; Tabrizi, Shervin; Rhoades, Justin; Blewett, Timothy; Xiong, Kan; Gydush, Gregory; Shea, Douglas; An, Zhenyi; Patel, Sahil; Cheng, Ju; Sridhar, Sainetra; Liu, Mei Hong; Lassen, Emilie; Skytte, Anne-Bine; Grońska-Pęski, Marta; Shoag, Jonathan E; Evrony, Gilad D; Parsons, Heather A; Mayer, Erica L; Makrigiorgos, G Mike; Golub, Todd R; Adalsteinsson, Viktor A
Detecting mutations from single DNA molecules is crucial in many fields but challenging. Next-generation sequencing (NGS) affords tremendous throughput but cannot directly sequence double-stranded DNA molecules ('single duplexes') to discern the true mutations on both strands. Here we present Concatenating Original Duplex for Error Correction (CODEC), which confers single duplex resolution to NGS. CODEC affords 1,000-fold higher accuracy than NGS, using up to 100-fold fewer reads than duplex sequencing. CODEC revealed mutation frequencies of 2.72 × 10-8 in sperm of a 39-year-old individual, and somatic mutations acquired with age in blood cells. CODEC detected genome-wide, clonal hematopoiesis mutations from single DNA molecules, single mutated duplexes from tumor genomes and liquid biopsies, microsatellite instability with 10-fold greater sensitivity and mutational signatures, and specific tumor mutations with up to 100-fold fewer reads. CODEC enables more precise genetic testing and reveals biologically significant mutations, which are commonly obscured by NGS errors.
PMID: 37106072
ISSN: 1546-1718
CID: 5465432