Cincinnati Children's Hospital Medical Center
Hassan Chaib
3333 Burnet Avenue
Cincinnati, OH 45229-3026
https://www.cincinnatichildrens.org/research/cores/dna-sequencing-genotyping
RRID: RRID:SCR_022630
1.) Farrow E, Rao S, Han SJ, Chang X, Huynh C, Brugmann SA, Lim HW, Tchieu J, Campbell K, Gebelein B (2026 Jan 7). An inducible system to study the regulatory functions of GSX2 in human lateral ganglionic eminence-like progenitors Developmental biology, 532(), 35-51. . PMCID: 12866604.
2.) Paulding D, Han SJ, Timmons J, Caye M, Riedel A, Brugmann SA, Barske L (2025 Nov 21). Cranial neural crest shortage leads to extensive craniofacial anomalies in mice mutant for the NR2F1/2 nuclear receptors Developmental biology, 530(), 102-118. . PMCID: 12720995.
3.) Granitto M, Parks L, Shook MS, Forney C, Chen X, Edsall LE, Donmez OA, Parameswaran S, Fisher KS, Zabeti A, Lawson LP, Weirauch MT, Kottyan LC (2025 Nov 12). Genome-wide discovery of multiple sclerosis genetic risk variant allelic regulatory activity. G3 (Bethesda, Md.), 15(11), . . PMCID: 12608076.
4.) Gill KK, Moore C, Nwogu O, Kroner JW, Chang W, Burkle J, Virolainen SJ, Stevens ML, Baatyrbek A kyzy, Miraldi ER, Biagini JM, Devonshire AL, Kottyan L, Schwartz JT, Assa'ad AH, Martin LJ, Andorf S, Khurana Hershey GK, Roskin KM (2025 Nov 11). B‐Cell Repertoire of Children With Atopic Dermatitis Exhibits Altered IgE Maturation Associated With Allergic Food Sensitization Allergy, 81(2), 513-523. . PMCID: 12862543.
5.) Caldwell JT, Shi T, Burg AR, Koby A, Roskin KM, Peters AL, DePasquale EA, Woodle ES, Hildeman DA (2025 Oct 24). CO-STIMULATORY BLOCKADE PREVENTS INTRAGRAFT ACCRUAL OF CLASS-SWITCHED, ACTIVATED B CELLS DESPITE FAILING TO PREVENT T-CELL MEDIATED REJECTION bioRxiv, (), 2025.10.24.683156. . PMCID: 12633403.
6.) Lee D, Abu-Shihab Y, Plas K, Nicolet D, Mrozek K, Routbort MJ, Patel KP, Walker CJ, Buss J, Stiff AR, Laganson A, DiNardo CD, Daver NG, Kadia TM, Ravandi F, Carroll AJ, Kolitz JE, Powell BL, Blum WG, Baer MR, Marcucci G, Uy GL, Stock W, Stone RM, Medeiros LJ, Byrd JC, Blachly JS, Bowman RL, Tyner JW, Loghavi S, Eisfeld AK, Miles LA (2025 Oct 15). Prognostic and Therapeutic Implications of BRAF Mutations in Acute Myeloid Leukemia bioRxiv, (), 2025.10.14.682328. . PMCID: 12632951.
7.) Solano AF, Preusse K, Cain B, Hotz R, Gavini P, Yuan Z, Bowen B, Maco G, Neal H, Gagliani EK, Ahn C, Lim HW, Southgate L, Kovall RA, Kopan R, Gebelein B (2025 Oct 7). Defective Notch1 signaling in endothelial cells drives pathogenesis in a mouse model of Adams-Oliver syndrome The Journal of Clinical Investigation, 135(23), e187532. . PMCID: 12646667.
8.) Edwards NA, Rankin SA, Kashyap A, Warren A, Agricola ZN, Kenny AP, Kofron M, Shen Y, Chung WK, Zorn AM (2025 Sep 22). Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in Xenopus trachea-esophageal morphogenesis. Developmental cell, 60(18), 2487-2502.e4. . PMID: 40412385.
9.) Durumutla HB, Haller A, Noble G, Prabakaran AD, McFarland K, Latimer H, Rajput A, Akinborewa O, Namjou-Khales B, Hui DY, Quattrocelli M (2025 Sep 2). The human glucocorticoid receptor variant rs6190 increases blood cholesterol and promotes atherosclerosis. The Journal of clinical investigation, 135(17), . . PMID: 40591411.
10.) Han SJY, Adani V, Farrow E, Parma B, Chang CF, Cochran K, Ramkissoon PJK, Esteban E, Elliott KH, Peterson KA, Gebelein BA, Garcia-Castro MI, Brugmann SA (2025 Aug 31). A dual role for GLI3 signaling in neural crest development. bioRxiv : the preprint server for biology, (), . . PMID: 40909740.
11.) Shook MS, Lu X, Chen X, Edsall LE, Granitto M, Virolainen SJ, Forney C, Donmez OA, Parameswaran S, Fadden C, Dexheimer PJ, Jenkins S, Grashel B, Kaufman KM, Hershey GK, Martin LJ, Satish L, Weirauch MT, Kottyan LC (2025 Aug 20). Massively parallel analysis of genotype-dependent enhancer activity among atopic dermatitis genetic risk variants. The Journal of allergy and clinical immunology, (), . pii: S0091-6749(25)00862-0. doi: 10.1016/j.jaci.2025.07.032. PMID: 40846081.
12.) Glaser K, Berklite L, Hickner BT, Rao P, Patel RH, Badachhape AA, Roy S, Schepers E, Timchenko NA, Geller JI, Ranganathan S, Tiao GM, Aronow B, Takebe T, Woodfield SE, Vasudevan SA, DePasquale EA, Bondoc AJ (2025 Aug 1). Oncogenic Role of Aberrant EZH2 in Hepatoblastoma bioRxiv, (), 2025.07.30.667506. . PMCID: 12324517.
13.) Clough CA, Cunningham C, Philbrook SY, Hueneman KM, Sampson AM, Choi K, Greis KD, Starczynowski D (2025 Aug). Characterization of E1 enzyme dependencies in mutant-UBA1 human cells reveals UBA6 as a novel therapeutic target in VEXAS syndrome. Leukemia, 39(8), 1997-2009. . PMID: 40588566.
14.) Bischoff LJ, Schrenk S, Soroko K, Boscolo E (2025 Jul 30). Expression of mutant TIE2 p.L914F during mouse development causes embryonic lethality and defects in vascular remodeling. bioRxiv : the preprint server for biology, (), . . PMID: 40766583.
15.) Dexheimer PJ, Hass MR, Edsall LE, Diouf AA, Jones SH, Donmez O, Yin C, Dunn KA, Forney C, Hesse HK, VonHandorf A, Chen X, Parameswaran S, Gittens OE, Viel KCMF, Razavi R, Gewurz BE, Zhao B, Lawson LP, Hughes TR, Kottyan LC, Weirauch MT (2025 Jul 30). Systematic investigation reveals extensive Epstein-Barr virus transcriptional regulation of the human genome. bioRxiv : the preprint server for biology, (), . . PMID: 40766721.
16.) Iwasawa K, Koike H, Al Reza H, Milton Y, Kishimoto K, Thorner K, Granitto M, Saiki N, Santangelo C, Glaser K, Kimura M, Bondoc A, Lim HW, Morimoto M, Iwafuchi M, Wells JM, Zorn AM, Takebe T (2025 Jun 8). Primitive Hepatoblasts Driving Early Liver Development bioRxiv, (), 2025.06.08.658502. . PMCID: 12157602.
17.) Agarwal P, Sampson A, Hueneman K, Choi K, Jakobsen NA, Uible E, Ishikawa C, Yeung J, Bolanos L, Zhao X, Setchell KD, Haslam DB, Galloway-Pena J, Byrd JC, Vyas P, Starczynowski DT (2025 Jun). Microbial metabolite drives ageing-related clonal haematopoiesis via ALPK1. Nature, 642(8066), 201-211. . PMID: 40269158.
18.) Kottyan LC, Richards S, Tracy ME, Lawson LP, Cobb B, Esslinger S, Gerwe M, Morgan J, Chandel A, Travitz L, Huang Y, Black C, Sobowale A, Akintobi T, Mitchell M, Beck AF, Unaka N, Seid M, Fairbanks S, Adams M, Mersha T, Namjou B, Pauciulo MW, Strawn JR, Ammerman RT, Santel D, Pestian J, Glauser T, Prows CA, Martin LJ, Muglia L, Harley JB, Chepelev I, Kaufman KM (2025 Mar 26). Sequencing and health data resource of children of African ancestry medRxiv, (), 2025.03.22.25324419. . PMCID: 11974803.
19.) Prabakaran AD, Chung HJ, McFarland K, Govindarajan T, Soussi FEA, Durumutla HB, Villa C, Piczer K, Latimer H, Werbrich C, Akinborewa O, Horning R, Quattrocelli M (2025 Jan 21). The human genetic variant rs6190 unveils Foxc1 and Arid5a as novel pro-metabolic targets of the glucocorticoid receptor in muscle. bioRxiv : the preprint server for biology, (), . . PMID: 38585940.
20.) Halurkar MS, Inoue O, Singh A, Mukherjee R, Ginugu M, Ahn C, Bonatto Paese CL, Duszynski M, Brugmann SA, Lim HW, Sanchez-Gurmaches J (2025 Jan 17). The widely used Ucp1-Cre transgene elicits complex developmental and metabolic phenotypes. Nature communications, 16(1), 770. . PMID: 39824816.
21.) Sunusi U, Osuji I, Ziegelmeyer B, Medvedovic M, Todd H, Abou-Khalil J, Zimmermann N (2025). The role of eosinophils and their activation state in hypereosinophilia-associated heart disease. Frontiers in immunology, 16(), 1635483. . PMCID: 12491288.
22.) Stiene DS, Osterburg AR, Corsarie LB, Balzarini NR, Medvedovic M, Borchers MT (2025). Inflammatory, Functional, and Compositional Changes of the Uterine Immune Microenvironment in a Lymphangioleiomyomatosis Mouse Model. Journal of cellular immunology, 7(3), 74-97. . PMID: 40893807.
23.) Tominaga K, Kechele DO, Sanchez JG, Vales S, Jurickova I, Roman L, Asai A, Enriquez JR, McCauley HA, Kishimoto K, Iwasawa K, Singh A, Horio Y, Múnera JO, Takebe T, Zorn AM, Helmrath MA, Denson LA, Wells JM (2024 Dec 17). Deriving Human Intestinal Organoids with Functional Tissue-Resident Macrophages All From Pluripotent Stem Cells Cellular and Molecular Gastroenterology and Hepatology, 19(4), 101444. . PMCID: 11847122.
24.) Durumutla HB, Haller A, Noble G, Prabakaran AD, McFarland K, Latimer H, Akinborewa O, Namjou-Khales B, Hui DY, Quattrocelli M (2024 Dec 3). The human glucocorticoid receptor variant rs6190 promotes blood cholesterol and atherosclerosis. bioRxiv : the preprint server for biology, (), . . PMID: 39677678.
25.) Marsili L, Duque KR, Abanto J, Chinchihualpa Paredes NO, Duker AP, Collins K, Miranda M, Bustamante ML, Pauciulo M, Dixon M, Chaib H, Perez-Maturo J, Hill EJ, Espay AJ, Kauffman MA (2024 Nov 23). Studying Rare Movement Disorders: From Whole-Exome Sequencing to New Diagnostic and Therapeutic Approaches in a Modern Genetic Clinic Biomedicines, 12(12), 2673. . PMCID: 11727247.
26.) Durumutla HB, Prabakaran AD, El Abdellaoui Soussi F, Akinborewa O, Latimer H, McFarland K, Piczer K, Werbrich C, Jain MK, Haldar SM, Quattrocelli M (2024 Nov 22). Glucocorticoid chronopharmacology promotes glucose metabolism in heart through a cardiomyocyte-autonomous transactivation program. JCI insight, 9(22), . . PMID: 39378111.
27.) Drucker M, Lee D, Zhang X, Kain B, Bowman M, Nicolet D, Wang Z, Stone RM, Mrózek K, Carroll AJ, Starczynowski DT, Levine RL, Byrd JC, Eisfeld AK, Salomonis N, Grimes HL, Bowman RL, Miles LA (2024 Nov 12). Genotype-immunophenotype relationships in NPM1-mutant AML clonal evolution uncovered by single cell multiomic analysis bioRxiv, (), 2024.11.11.623033. . PMCID: 11601460.
28.) He H, Bell SM, Davis AK, Zhao S, Sridharan A, Na CL, Guo M, Xu Y, Snowball J, Swarr DT, Zacharias WJ, Whitsett JA (2024 Sep 16). PRDM3/16 regulate chromatin accessibility required for NKX2-1 mediated alveolar epithelial differentiation and function Nature Communications, 15(), 8112. . PMCID: 11405758.
29.) DeVore SB, Schuetz M, Alvey L, Lujan H, Ochayon DE, Williams L, Chang WC, Filuta A, Ruff B, Kothari A, Hahn JM, Brandt E, Satish L, Roskin K, Herr AB, Biagini JM, Martin LJ, Cagdas D, Keles S, Milner JD, Supp DM, Khurana Hershey GK (2024 Aug 27). Regulation of MYC by CARD14 in human epithelium is a determinant of epidermal homeostasis and disease. Cell reports, 43(8), 114589. . PMID: 39110589.
30.) Sunusi U, Ziegelmeyer B, Osuji I, Medvedovic M, Todd H, Abou-Khalil J, Zimmermann N (2024 Jul 5). Pathophysiology of hypereosinophilia-associated heart disease. bioRxiv : the preprint server for biology, (), . . PMID: 39005455.
31.) Stepanchick E, Wilson A, Sulentic AM, Choi K, Hueneman K, Starczynowski DT, Chlon TM (2024 Jun 27). DDX41 haploinsufficiency causes inefficient hematopoiesis under stress and cooperates with p53 mutations to cause hematologic malignancy Leukemia, 38(8), 1787-1798. . PMCID: 11286521.
32.) Sayeed K, Parameswaran S, Beucler MJ, Edsall LE, VonHandorf A, Crowther A, Donmez O, Hass M, Richards S, Forney C, Wright J, Leong MML, Murray-Nerger LA, Gewurz BE, Kaufman KM, Harley JB, Zhao B, Miller WE, Kottyan LC, Weirauch MT (2024 May 22). Human cytomegalovirus infection coopts chromatin organization to diminish TEAD1 transcription factor activity. bioRxiv : the preprint server for biology, (), . . PMID: 38645179.
33.) Prabakaran AD, McFarland K, Miz K, Durumutla HB, Piczer K, El Abdellaoui Soussi F, Latimer H, Werbrich C, Chung HJ, Blair NS, Millay DP, Morris AJ, Prideaux B, Finck BN, Quattrocelli M (2024 May 3). Intermittent glucocorticoid treatment improves muscle metabolism via the PGC1α/Lipin1 axis in an aging-related sarcopenia model. The Journal of clinical investigation, 134(11), . . PMID: 38702076.
34.) Xu N, Alfieri CM, Yu Y, Guo M, Yutzey KE (2024 Apr 25). Wnt Signaling Inhibition Prevents Postnatal Inflammation and Disease Progression in Mouse Congenital Myxomatous Valve Disease Arteriosclerosis, thrombosis, and vascular biology, 44(7), 1540-1554. . PMCID: 11209782.
35.) Virolainen SJ, Satish L, Biagini JM, Chaib H, Chang WC, Dexheimer PJ, Dixon MR, Dunn K, Fletcher D, Forney C, Granitto M, Hestand MS, Hurd M, Kauffman K, Lawson L, Martin LJ, Peña LD, Phelan KJ, Shook M, Weirauch MT, Khurana Hershey GK, Kottyan LC (2024 Apr 2). Filaggrin loss-of-function variants are associated with atopic dermatitis phenotypes in a diverse, early-life prospective cohort JCI Insight, 9(9), e178258. . PMCID: 11141906.
36.) Viel KCMF, Parameswaran S, Donmez OA, Forney CR, Hass MR, Yin C, Jones SH, Prosser HK, Diouf AA, Gittens OE, Edsall LE, Chen X, Rowden H, Dunn KA, Guo R, VonHandorf A, Leong MML, Ernst K, Kaufman KM, Lawson LP, Gewurz B, Zhao B, Kottyan LC, Weirauch MT (2024 Mar 12). Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome. BMC genomics, 25(1), 273. . PMID: 38475709.
37.) El Abdellaoui Soussi F, Durumutla HB, Latimer H, Prabakaran AD, McFarland K, Miz K, Piczer K, Werbrich C, Jain MK, Haldar SM, Quattrocelli M (2023 Dec 23). Light-phase prednisone promotes glucose oxidation in heart through novel transactivation targets of cardiomyocyte-specific GR and KLF15. bioRxiv : the preprint server for biology, (), . . PMID: 38187555.
38.) Pode-Shakked N, Slack M, Sundaram N, Schreiber R, McCracken KW, Dekel B, Helmrath M, Kopan R (2023 Dec 9). RAAS-deficient organoids indicate delayed angiogenesis as a possible cause for autosomal recessive renal tubular dysgenesis. Nature communications, 14(1), 8159. . PMID: 38071212.
39.) Edwards NA, Kashyap A, Warren A, Agricola ZN, Kenny AP, Shen Y, Chung WK, Zorn AM (2023 Nov 21). Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in trachea-esophageal morphogenesis. bioRxiv : the preprint server for biology, (), . . PMID: 37873300.
40.) Múnera JO, Kechele DO, Bouffi C, Qu N, Jing R, Maity P, Enriquez JR, Han L, Campbell I, Mahe MM, McCauley HA, Zhang X, Sundaram N, Hudson JR, Zarsozo-Lacoste A, Pradhan S, Tominaga K, Sanchez JG, Weiss AA, Chatuvedi P, Spence JR, Hachimi M, North T, Daley GQ, Mayhew CN, Hu YC, Takebe T, Helmrath MA, Wells JM (2023 Nov 2). Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon Cell stem cell, 30(11), 1434-1451.e9. . PMCID: 10913028.
41.) Prabakaran AD, McFarland K, Miz K, Durumutla HB, Piczer K, El Abdellaoui Soussi F, Latimer H, Werbrich C, Blair NS, Millay DP, Prideaux B, Finck BN, Quattrocelli M (2023 Oct 19). Glucocorticoid intermittence coordinates rescue of energy and mass in aging-related sarcopenia through the myocyte-autonomous PGC1alpha-Lipin1 transactivation. bioRxiv : the preprint server for biology, (), . . PMID: 37905062.
42.) Shi T, Burg AR, Caldwell JT, Roskin KM, Castro-Rojas CM, Chukwuma PC, Gray GI, Foote SG, Alonso JA, Cuda CM, Allman DA, Rush JS, Regnier CH, Wieczorek G, Alloway RR, Shields AR, Baker BM, Woodle ES, Hildeman DA (2023 Jul 17). Single-cell transcriptomic analysis of renal allograft rejection reveals insights into intragraft TCR clonality The Journal of Clinical Investigation, 133(14), e170191. . PMCID: 10348771.
43.) Shanmuganad S, Ferguson A, Paranjpe A, Cianciolo EE, Katz JD, Herold MJ, Hildeman DA (2023 Mar 2). Subset-specific and temporal control of effector and memory CD4+ T cell survival. bioRxiv : the preprint server for biology, (), . . PMID: 36909576.
44.) Shi T, Burg AR, Caldwell JT, Roskin K, Castro-Rojas CM, Chukwuma PC, Gray GI, Foote SG, Alonso J, Cuda CM, Allman DA, Rush JS, Regnier CH, Wieczorek G, Alloway RR, Shields AR, Baker BM, Woodle ES, Hildeman DA (2023 Feb 13). Single cell transcriptomic analysis of renal allograft rejection reveals novel insights into intragraft TCR clonality. bioRxiv : the preprint server for biology, (), . . PMID: 36798151.
45.) Khorki ME, Shi T, Cianciolo EE, Burg AR, Chukwuma PC, Picarsic JL, Morrice MK, Woodle ES, Maltzman JS, Ferguson A, Katz JD, Baker BM, Hildeman DA (2023). Prior viral infection primes cross-reactive CD8+ T cells that respond to mouse heart allografts. Frontiers in immunology, 14(), 1287546. . PMID: 38143762.
Serving the CCHMC and UC research community since 2001, the Genomics Sequencing Facility is an institutional resource for genomics services and data generation utilizing state-of-the-art instrumentation and methods. With more than 50 years of laboratory experience by our staff, we are proficient in many types of library preparations, size selection, library pooling, sequencing and genotyping techniques. We have recently launched a new sftp file download server for NGS results files to help facilitate rapid file downloads for large numbers of files, or large file sizes.
