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Haller M, Yin Y, Haller G, Li T, Li Q, Lamb LE, Ma L. Streamlined identification of clinically and functionally relevant genetic regulators of lower-tract urogenital development. Proc Natl Acad Sci U S A 2024; 121:e2309466121. [PMID: 38300866 PMCID: PMC10861909 DOI: 10.1073/pnas.2309466121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 12/18/2023] [Indexed: 02/03/2024] Open
Abstract
Congenital anomalies of the lower genitourinary (LGU) tract are frequently comorbid due to genetically linked developmental pathways, and are among the most common yet most socially stigmatized congenital phenotypes. Genes involved in sexual differentiation are prime candidates for developmental anomalies of multiple LGU organs, but insufficient prospective screening tools have prevented the rapid identification of causative genes. Androgen signaling is among the most influential modulators of LGU development. The present study uses SpDamID technology in vivo to generate a comprehensive map of the pathways actively regulated by the androgen receptor (AR) in the genitalia in the presence of the p300 coactivator, identifying wingless/integrated (WNT) signaling as a highly enriched AR-regulated pathway in the genitalia. Transcription factor (TF) hits were then assayed for sexually dimorphic expression at two critical time points and also cross-referenced to a database of clinically relevant copy number variations to identify 252 TFs exhibiting copy variation in patients with LGU phenotypes. A subset of 54 TFs was identified for which LGU phenotypes are statistically overrepresented as a proportion of total observed phenotypes. The 252 TF hitlist was then subjected to a functional screen to identify hits whose silencing affects genital mesenchymal growth rates. Overlap of these datasets results in a refined list of 133 TFs of both functional and clinical relevance to LGU development, 31 of which are top priority candidates, including the well-documented renal progenitor regulator, Sall1. Loss of Sall1 was examined in vivo and confirmed to be a powerful regulator of LGU development.
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Affiliation(s)
- Meade Haller
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Yan Yin
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Gabe Haller
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO63110
| | - Tian Li
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Qiufang Li
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Laura E. Lamb
- Department of Urology, William Beaumont School of Medicine, Oakland University, Rochester, MI48309
| | - Liang Ma
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
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2
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Minto M, Sotelo-Fonseca JE, Ramesh V, West AE. Genome binding properties of Zic transcription factors underlie their changing functions during neuronal maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574185. [PMID: 38260638 PMCID: PMC10802290 DOI: 10.1101/2024.01.04.574185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background The Zic family of transcription factors (TFs) promote both proliferation and maturation of cerebellar granule neurons (CGNs), raising the question of how a single, constitutively expressed TF family can support distinct developmental processes. Here we use an integrative experimental and bioinformatic approach to discover the regulatory relationship between Zic TF binding and changing programs of gene transcription during CGN differentiation. Results We first established a bioinformatic pipeline to integrate Zic ChIP-seq data from the developing mouse cerebellum with other genomic datasets from the same tissue. In newborn CGNs, Zic TF binding predominates at active enhancers that are co-bound by developmentally-regulated TFs including Atoh1, whereas in mature CGNs, Zic TF binding consolidates toward promoters where it co-localizes with activity-regulated TFs. We then performed CUT&RUN-seq in differentiating CGNs to define both the time course of developmental shifts in Zic TF binding and their relationship to gene expression. Mapping Zic TF binding sites to genes using chromatin looping, we identified the set of Zic target genes that have altered expression in RNA-seq from Zic1 or Zic2 knockdown CGNs. Conclusion Our data show that Zic TFs are required for both induction and repression of distinct, developmentally regulated target genes through a mechanism that is largely independent of changes in Zic TF binding. We suggest that the differential collaboration of Zic TFs with other TF families underlies the shift in their biological functions across CGN development.
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Affiliation(s)
- Melyssa Minto
- Duke University, Program in Computational Biology and Bioinformatics, Durham, NC 27710
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC 27709
| | | | | | - Anne E. West
- Duke University, Department of Neurobiology, Durham, NC 27710
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Eisenberg ML, Esteves SC, Lamb DJ, Hotaling JM, Giwercman A, Hwang K, Cheng YS. Male infertility. Nat Rev Dis Primers 2023; 9:49. [PMID: 37709866 DOI: 10.1038/s41572-023-00459-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
Clinical infertility is the inability of a couple to conceive after 12 months of trying. Male factors are estimated to contribute to 30-50% of cases of infertility. Infertility or reduced fertility can result from testicular dysfunction, endocrinopathies, lifestyle factors (such as tobacco and obesity), congenital anatomical factors, gonadotoxic exposures and ageing, among others. The evaluation of male infertility includes detailed history taking, focused physical examination and selective laboratory testing, including semen analysis. Treatments include lifestyle optimization, empirical or targeted medical therapy as well as surgical therapies that lead to measurable improvement in fertility. Although male infertility is recognized as a disease with effects on quality of life for both members of the infertile couple, fewer data exist on specific quantification and impact compared with other health-related conditions.
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Affiliation(s)
- Michael L Eisenberg
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Obstetrics & Gynecology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Sandro C Esteves
- ANDROFERT Andrology and Human Reproduction Clinic, Campinas, Brazil
- Division of Urology, Department of Surgery, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Dolores J Lamb
- Center for Reproductive Genomics, Weill Cornell Medical College, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Urology, Weill Cornell Medical College, New York, NY, USA
| | - James M Hotaling
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Kathleen Hwang
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Yu-Sheng Cheng
- Department of Urology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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Ruthig VA, Lamb DJ. Modeling development of genitourinary birth defects to understand disruption due to changes in gene dosage. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2022; 10:412-424. [PMID: 36636694 PMCID: PMC9831917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 01/14/2023]
Abstract
Genitourinary development is a delicately orchestrated process that begins in the embryo. Once complete, the genitourinary system is a collection of functionally disparate organs spread throughout the abdominal and pelvic regions. These distinct organs are interconnected through an elaborate duct system which aggregates the organs' products to a common exit point. The complicated nature of the genitourinary system makes it highly susceptible to developmental disruptions that produce anomalies. In fact, genitourinary anomalies are among the most common class of human birth defects. Aside from congenital anomalies of the kidney and urinary tract (CAKUT), for males, these birth defects can also occur in the penis (hypospadias) and testis (cryptorchism), which impact male fertility and male mental health. As genetic technology has advanced, it has become clear that a subset of cases of genitourinary birth defects are due to gene variation causing dosage changes in critical regulatory genes. Here we first review the parallels between human and mouse genitourinary development. We then demonstrate how translational research leverages mouse models of human gene variation cases to advance mechanistic understanding of causation in genitourinary birth defects. We close with a view to the future highlighting upcoming technologies that will provide a deeper understanding of gene variation affecting regulation of genitourinary development, which should ultimately advance treatment options for patients.
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Affiliation(s)
- Victor A Ruthig
- Department of Urology, Weill Cornell MedicineNew York, NY, USA,Sexual Medicine Laboratory, Weill Cornell MedicineNew York, NY, USA
| | - Dolores J Lamb
- Department of Urology, Weill Cornell MedicineNew York, NY, USA,Center for Reproductive Genomics, Weill Cornell MedicineNew York, NY, USA,Englander Institute for Precision Medicine, Weill Cornell MedicineNew York, NY, USA
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5
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A multi-omics longitudinal study of the murine retinal response to chronic low-dose irradiation and simulated microgravity. Sci Rep 2022; 12:16825. [PMID: 36207342 PMCID: PMC9547011 DOI: 10.1038/s41598-022-19360-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/29/2022] [Indexed: 11/18/2022] Open
Abstract
The space environment includes unique hazards like radiation and microgravity which can adversely affect biological systems. We assessed a multi-omics NASA GeneLab dataset where mice were hindlimb unloaded and/or gamma irradiated for 21 days followed by retinal analysis at 7 days, 1 month or 4 months post-exposure. We compared time-matched epigenomic and transcriptomic retinal profiles resulting in a total of 4178 differentially methylated loci or regions, and 457 differentially expressed genes. Highest correlation in methylation difference was seen across different conditions at the same time point. Nucleotide metabolism biological processes were enriched in all groups with activation at 1 month and suppression at 7 days and 4 months. Genes and processes related to Notch and Wnt signaling showed alterations 4 months post-exposure. A total of 23 genes showed significant changes in methylation and expression compared to unexposed controls, including genes involved in retinal function and inflammatory response. This multi-omics analysis interrogates the epigenomic and transcriptomic impacts of radiation and hindlimb unloading on the retina in isolation and in combination and highlights important molecular mechanisms at different post-exposure stages.
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Yang R, Zuo L, Ma H, Zhou Y, Zhou P, Wang L, Wang M, Latif M, Kong L. Downregulation of nc886 contributes to prostate cancer cell invasion and TGFβ1-induced EMT. Genes Dis 2022; 9:1086-1098. [PMID: 35685460 PMCID: PMC9170576 DOI: 10.1016/j.gendis.2020.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/09/2020] [Accepted: 12/24/2020] [Indexed: 11/16/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) activation is important in cancer progression and metastasis. Evidence indicates that nc886 is a representative Pol III gene that processes microRNA products via Dicer and further downregulates its target gene transforming growth factor- β1 (TGF-β1), which is the most prominent inducer of EMT in prostate cancer (PC). Consistent with the previous literature, we found that nc886 downregulation was strongly associated with metastatic behavior and showed worse outcomes in PC patients. However, little is known about the association between nc886 and the EMT signaling pathway. We developed a PC cell model with stable overexpression of nc886 and found that nc886 changed cellular morphology and drove MET. The underlying mechanism may be related to its promotion of SNAIL protein degradation via ubiquitination, but not to its neighboring genes, TGFβ-induced protein (TGFBI) and SMAD5, which are Pol II-transcribed. TGF-β1 also override nc886 promotion of MET via transient suppression the transcription of nc886, promotion of TGFBI or increase in SMAD5 phosphorylation. Both nc886 inhibition and TGFBI activation occur regardless of their methylation status. The literature suggests that MYC inhibition by TGF-β1 is attributed to nc886 downregulation. We incidentally identified MYC-associated zinc finger protein (MAZ) as a suppressive transcription factor of TGFBI, which is controlled by TGF-β1. We elucidate a new mechanism of TGF-β1 differential control of Pol II and the transcription of its neighboring Pol III gene and identify a new EMT unit consisting of nc886 and its neighboring genes.
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Affiliation(s)
- Ronghui Yang
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, PR China
| | - Lingkun Zuo
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, PR China
| | - Hui Ma
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, PR China
| | - Ying Zhou
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, PR China
| | - Ping Zhou
- Biomedical Engineering Institute of Capital Medical University, Capital Medical University, Beijing 100069, PR China
| | - Liyong Wang
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, PR China
| | - Miao Wang
- Department of Pathology, Beijing Friendship Hospital, The Second Clinical Medical College of Capital Medical University, Beijing 100050, PR China
| | - Mahrukh Latif
- Department of Nuclear Medicine, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050010, PR China
| | - Lu Kong
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, PR China
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Ortabozkoyun H, Huang PY, Cho H, Narendra V, LeRoy G, Gonzalez-Buendia E, Skok JA, Tsirigos A, Mazzoni EO, Reinberg D. CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters. Nat Genet 2022; 54:202-212. [PMID: 35145304 PMCID: PMC8837555 DOI: 10.1038/s41588-021-01008-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 12/22/2021] [Indexed: 12/14/2022]
Abstract
CCCTC-binding factor (CTCF) is critical to three-dimensional genome organization. Upon differentiation, CTCF insulates active and repressed genes within Hox gene clusters. We conducted a genome-wide CRISPR knockout (KO) screen to identify genes required for CTCF-boundary activity at the HoxA cluster, complemented by biochemical approaches. Among the candidates, we identified Myc-associated zinc-finger protein (MAZ) as a cofactor in CTCF insulation. MAZ colocalizes with CTCF at chromatin borders and, similar to CTCF, interacts with the cohesin subunit RAD21. MAZ KO disrupts gene expression and local contacts within topologically associating domains. Similar to CTCF motif deletions, MAZ motif deletions lead to derepression of posterior Hox genes immediately after CTCF boundaries upon differentiation, giving rise to homeotic transformations in mouse. Thus, MAZ is a factor contributing to appropriate insulation, gene expression and genomic architecture during development.
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Affiliation(s)
- Havva Ortabozkoyun
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Pin-Yao Huang
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Hyunwoo Cho
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA.,Department of Radiation Oncology, NYU Grossman School of Medicine, New York, NY, USA
| | - Varun Narendra
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gary LeRoy
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Edgar Gonzalez-Buendia
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Jane A Skok
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA.,Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Danny Reinberg
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA. .,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA.
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8
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Zheng C, Wu H, Jin S, Li D, Tan S, Zhu X. Roles of Myc-associated zinc finger protein in malignant tumors. Asia Pac J Clin Oncol 2022; 18:506-514. [PMID: 35098656 DOI: 10.1111/ajco.13748] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/04/2021] [Indexed: 11/30/2022]
Abstract
As an important transcription factor that is widely expressed in most tissues of the human body, Myc-associated zinc finger protein (MAZ) has been reported highly expressed in many malignant tumors and thought to be a promising therapeutic target for cancer treatment. In this review, we aim to offer a comprehensive understanding of MAZ regulation in malignant tumors. The carboxy terminal of MAZ protein contains six C2H2 zinc fingers, and its regulation of transcription is based on the interaction between the GC-rich DNA binding sites of target genes and its carboxy-terminal zinc finger motifs. MAZ protein has been found to activate or inhibit the transcriptional initiation process of many target genes, as well as play an important role in the transcriptional termination process of some target genes, so MAZ poses dual regulatory functions in the initiation and termination process of gene transcription. Through the transcriptional regulation of c-myc and Ras gene family, MAZ poses an important role in the occurrence and development of breast cancer, pancreatic cancer, prostate cancer, glioblastoma, neuroblastoma, and other malignant tumors. Our review shows a vital role of MAZ in many malignant tumors and provides novel insight for cancer diagnosis and treatment.
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Affiliation(s)
- Chuanjun Zheng
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Hongmei Wu
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Song Jin
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Di Li
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Shengkui Tan
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Xiaonian Zhu
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
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Punjani N, Kang C, Lamb DJ, Schlegel PN. Current updates and future perspectives in the evaluation of azoospermia: A systematic review. Arab J Urol 2021; 19:206-214. [PMID: 34552771 PMCID: PMC8451618 DOI: 10.1080/2090598x.2021.1954415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Objectives: To provide a summary of the current evaluation of azoospermia and insights into future perspectives in the evaluation and counselling of men with azoospermia. Methods: A search of PubMed, Cochrane Reviews and Web of Science databases was performed for full-text English-language articles published between 1943 and 2020 focussing on ‘future perspectives’, ‘azoospermia’ and ‘evaluation’. Results: Azoospermia represents a severe form of male infertility characterised by sperm production so impaired that there are no sperm present in the ejaculate. The current evaluation of azoospermia focusses on patient history and physical examination with selected adjunctive laboratory investigations including serum hormones, a karyotype and screening for Y chromosome microdeletions. Future diagnostics are focussed on identifying the underlying genetic aetiologies for azoospermia, as well as a greater emphasis on screening for systemic illness that men with severe infertility may be predisposed to develop. Conclusion: Azoospermia represents an extreme form of male infertility, and evaluation relies heavily on history and physical examination, as genetic evaluations for these individuals remain limited. Future evaluation will focus on next-generation sequencing and more rigorous evaluation for possible co-existing and future risk of systemic disease. ABBREVIATIONS: ADGRG2, adhesion G protein-coupled receptor G2; ASRM: American Society of Reproductive Medicine; AZF: azoospermia factor; CBAVD: congenital bilateral absence of the vas deferens; CFTR: cystic fibrosis transmembrane conductance regulator; CRKL: CRK-like proto-oncogene; E2F1: E2F transcription factor 1; HAUS7: HAUS augmin-like complex subunit 7; HR: hazard ratio; KS: Klinefelter syndrome; MAZ, MYC-associated zinc finger protein; NGS: next-generation sequencing; NOA: non-obstructive azoospermia; OA: obstructive azoospermia; RHOX: reproductive homeobox on the X chromosome; SH2: SRC homology 2; TAF7L: TATA-box binding protein associated factor 7-like; TEX11: testis-expressed 11; WES: whole-exome sequencing
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Affiliation(s)
- Nahid Punjani
- Department of Urology, Weill Cornell Medical College, New York, NY, USA
| | - Caroline Kang
- Department of Urology, Weill Cornell Medical College, New York, NY, USA
| | - Dolores J Lamb
- Department of Urology, Weill Cornell Medical College, New York, NY, USA.,Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, NY, USA.,Center for Reproductive Genomics, Weill Cornell Medical College, New York, NY, USA
| | - Peter N Schlegel
- Department of Urology, Weill Cornell Medical College, New York, NY, USA.,Center for Reproductive Genomics, Weill Cornell Medical College, New York, NY, USA
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