Spatial & Functional
Genomics Affinity Group

SFG Publications

A UVB-responsive common variant at chromosome band 7p21.1 confers tanning response and melanoma risk via regulation of the aryl hydrocarbon receptor, AHR

Mai Xu, Lindsey Mehl, Tongwu Zhang, Rohit Thakur, Hayley Sowards, Timothy Myers, Lea Jessop, Alessandra Chesi, Matthew E Johnson, Andrew D Wells, Helen T Michael, Patricia Bunda, Kristine Jones, Herbert Higson, Rebecca C Hennessey, Ashley Jermusyk, Michael A Kovacs, Maria Teresa Landi, Mark M Iles, Alisa M Goldstein, Melanoma Meta-Analysis Consortium; Jiyeon Choi, Stephen J Chanock, Struan F A Grant, Raj Chari, Glenn Merlino, Matthew H Law, Kevin M Brown

The American Journal of Human Genetics, Volume 108, Issue 9, Pages 1611-1630, September 2, 2021

PMID: 34343493

Restriction enzyme selection dictates detection range sensitivity in chromatin conformation capture-based variant-to-gene mapping approaches

Chun Su, Matthew C Pahl, Struan F A Grant, Andrew D Wells

Human Genetics, August 18, 2021

PMID: 34405268

Identification of 22 susceptibility loci associated with testicular germ cell tumors

John Pluta, Louise C Pyle, Kevin T Nead, Rona Wilf, Mingyao Li, Nandita Mitra, Benita Weathers, Kurt D'Andrea, Kristian Almstrup, Lynn Anson-Cartwright, Javier Benitez, Christopher D Brown, Stephen Chanock, Chu Chen, Victoria K Cortessis, Alberto Ferlin, Carlo Foresta, Marija Gamulin, Jourik A Gietema, Chiara Grasso, Mark H Greene, Tom Grotmol, Robert J Hamilton, Trine B Haugen, Russ Hauser, Michelle A T Hildebrandt, Matthew E Johnson, Robert Karlsson, Lambertus A Kiemeney, Davor Lessel, Ragnhild A Lothe, Jennifer T Loud, Chey Loveday, Paloma Martin-Gimeno, Coby Meijer, Jérémie Nsengimana, David I Quinn, Thorunn Rafnar, Shweta Ramdas, Lorenzo Richiardi, Rolf I Skotheim, Kari Stefansson, Clare Turnbull, David J Vaughn, Fredrik Wiklund, Xifeng Wu, Daphne Yang, Tongzhang Zheng, Andrew D Wells, Struan F A Grant, Ewa Rajpert-De Meyts, Stephen M Schwartz, D Timothy Bishop, Katherine A McGlynn, Peter A Kanetsky, Katherine L Nathanson, Testicular Cancer Consortium

Nature Communications volume 12, Article number: 4487, July 23, 2021

PMID: 34301922

CRISPR-Cas9–Mediated Genome Editing Confirms EPDR1 as an Effector Gene at the BMD GWAS-Implicated ‘STARD3NL’ Locus

James A Pippin, Alessandra Chesi, Yadav Wagley, Chun Su, Matthew C Pahl, Kenyaita M Hodge, Matthew E Johnson, Andrew D Wells, Kurt D Hankenson, Struan F A Grant

JBMR Plus, July 5, 2021

PMID: 34532616

Large trans-ethnic meta-analysis identifies AKR1C4 as a novel gene associated with age at menarche

C Sarnowski, D L Cousminer, N Franceschini, L M Raffield, G Jia, L Fernández-Rhodes, S F A Grant, H Hakonarson, L A Lange, J Long, T Sofer, R Tao, R B Wallace, Q Wong, G Zirpoli, E Boerwinkle, J P Bradfield, A Correa, C L Kooperberg, K E North, J R Palmer, B S Zemel, W Zheng, J M Murabito, K L Lunetta

Human Reproduction, Volume 36, Issue 7, July 2021, Pages 1999–2010,  May 22, 2021

PMID: 34021356

Constrained chromatin accessibility in PU.1-mutated agammaglobulinemia patients

Carole Le Coz, David N Nguyen, Chun Su, Brian E Nolan, Amanda V Albrecht, Suela Xhani, Di Sun, Benjamin Demaree, Piyush Pillarisetti, Caroline Khanna, Francis Wright, Peixin Amy Chen, Samuel Yoon, Amy L Stiegler, Kelly Maurer, James P Garifallou, Amy Rymaszewski, Steven H Kroft, Timothy S Olson, Alix E Seif, Gerald Wertheim, Struan F A Grant, Linda T Vo, Jennifer M Puck, Kathleen E Sullivan, John M Routes, Viktoria Zakharova, Anna Shcherbina, Anna Mukhina, Natasha L Rudy, Anna C E Hurst, T Prescott Atkinson, Titus J Boggon, Hakon Hakonarson, Adam R Abate, Joud Hajjar, Sarah K Nicholas, James R Lupski, James Verbsky, Ivan K Chinn, Michael V Gonzalez, Andrew D Wells, Alex Marson, Gregory M K Poon, Neil Romberg

J Exp Med (2021) 218 (7): e20201750.    May 05 2021.

PMID: 33951726

Colorectal cancer-associated Smad4 R361 hotspot mutations boost Wnt/β-catenin signaling through enhanced Smad4-LEF1 binding

Claudia B Lanauze, Priyanka Sehgal, Katharina Hayer, Manuel Torres-Diz, James A Pippin, Struan F A Grant and Andrei Thomas-Tikhonenko

Mol Cancer Res February 19 2021

PMID: 33608451

3D promoter architecture re-organization during iPSC-derived neuronal cell differentiation implicates target genes for neurodevelopmental disorders

Chun Su, Mariana Argenziano, Sumei Lu, James A Pippin, Matthew C Pahl, Michelle E Leonard, Diana L Cousminer, Matthew E Johnson, Chiara Lasconi, Andrew D Wells, Alessandra Chesi, Struan F A Grant

Progress in Neurobiology, p102000,  January 23, 2021

PMID: 33545232

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal additional BMI loci

Reza K Hammond, Matthew C Pahl, Chun Su, Diana L Cousminer, Michelle E Leonard, Sumei Lu, Claudia A Doege, Yadav Wagley, Kenyaita M Hodge, Chiara Lasconi, Matthew E Johnson, James A Pippin, Kurt D Hankenson, Rudolph L Leibel, Alessandra Chesi, Andrew D Wells, Struan FA Grant

eLife 2021; Vol 10, pp1334-19, January 18, 2021

PMID: 33459256

Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual

Diana L. Cousminer*† , Yadav Wagley†, James A. Pippin†, Ahmed Elhakeem, Gregory P. Way, Matthew C. Pahl, Shana E. McCormack, Alessandra Chesi, Jonathan A. Mitchell, Joseph M. Kindler, Denis Baird, April Hartley, Laura Howe, Heidi J. Kalkwarf, Joan M. Lappe, Sumei Lu, Michelle E. Leonard, Matthew E. Johnson, Hakon Hakonarson, Vicente Gilsanz, John A. Shepherd, Sharon E. Oberfield, Casey S. Greene, Andrea Kelly, Deborah A. Lawlor, Benjamin F. Voight, Andrew D. Wells, Babette S. Zemel, Kurt D. Hankenson*† and Struan F. A. Grant*†

Genome Biology, volume 22, Article number: 1, January 4, 2021

PMID: 33397451

Pages