Spatial & Functional
Genomics Affinity Group

SFG Publications

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:

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, 2021 p 102000

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

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 2021 Jan 4;22(1):1

PMID: 33397451

Variant-to-Gene-Mapping Analyses Reveal a Role for the Hypothalamus in Genetic Susceptibility to Inflammatory Bowel Disease

Chiara Lasconi, Matthew C Pahl, Diana L Cousminer, Claudia A Doege, Alessandra Chesi, Kenyaita M Hodge, Michelle E Leonard, Sumei Lu, Matthew E Johnson, Chun Su, Reza K Hammond, James A Pippin, Natalie A Terry, Louis R Ghanem, Rudolph L Leibel, Andrew D Wells, Struan F A Grant

Cellular and Molecular Gastroenterology and Hepatology, 2020 pp1-16

PMID: 33069917

Mapping effector genes at lupus GWAS loci using promoter Capture-C in follicular helper T cells

Chun Su, Matthew E. Johnson, Annabel Torres, Rajan M. Thomas, Elisabetta Manduchi, Prabhat Sharma, Parul Mehra, Carole Le Coz, Michelle E. Leonard, Sumei Lu, Kenyaita M. Hodge, Alessandra Chesi, James Pippin, Neil Romberg, Struan F. A. Grant & Andrew D. Wells

Nature Communications volume 11, Article number: 3294 (2020)

PMID: 32620744

Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant complex traits

Matthew C. Pahl, Claudia A. Doege, Kenyaita M. Hodge, Sheridan H. Littleton, Michelle E. Leonard, Sumei Lu, Rick Rausch, James A. Pippin, Jonathan P. Bradfield, Reza K. Hammond, Keith Boehm, Robert I. Berkowitz, Chiara Lasconi, Chun Su, Alessandra Chesi, Matthew E. Johnson, Andrew D. Wells, Benjamin F. Voight, Rudolph L. Leibel, Diana L. Cousminer, Struan F.A. Grant

doi: https://doi.org/10.1101/2020.07.06.146951

PMID: BioRxiv

The Genetic Contribution to Type 1 Diabetes.

Bakay M1, Pandey R1, Grant SFA1,2,3,4, Hakonarson H5,6.

 

Curr Diab Rep. 2019 Nov 4;19(11):116.

doi: 10.1007/s11892-019-1235-1.

PMID: 31686270

Associations of autozygosity with a broad range of human phenotypes.

Clark DW1, Okada Y2,3,4, Moore KHS5, Mason D6, Pirastu N1, Gandin I7,8, Mattsson H9,10, Barnes CLK1, Lin K11, Zhao JH12,13, Deelen P14, Rohde R15, Schurmann C16, Guo X17, Giulianini F18, Zhang W19,20, Medina-Gomez C21,22,23, Karlsson R24, Bao Y25, Bartz TM26, Baumbach C27, Biino G28, Bixley MJ29, Brumat M8, Chai JF30, Corre T31,32,33, Cousminer DL34,35, Dekker AM36, Eccles DA37,38, van Eijk KR36, Fuchsberger C39, Gao H19,40, Germain M41,42, Gordon SD43, de Haan HG44, Harris SE45,46, Hofer E47,48, Huerta-Chagoya A49, Igartua C50, Jansen IE51,52, Jia Y17, Kacprowski T53,54, Karlsson T55, Kleber ME56, Li SA57, Li-Gao R44, Mahajan A58, Matsuda K59, Meidtner K60,61, Meng W62, Montasser ME63,64, van der Most PJ65, Munz M66,67,68,69, Nutile T70, Palviainen T71, Prasad G72, Prasad RB73, Priyanka TDS74, Rizzi F75,76, Salvi E76,77, Sapkota BR78, Shriner D79, Skotte L80, Smart MC25, Smith AV81,82, van der Spek A22, Spracklen CN83, Strawbridge RJ84,85, Tajuddin SM86, Trompet S87,88, Turman C89,90, Verweij N91, Viberti C92, Wang L93, Warren HR94,95, Wootton RE96,97, Yanek LR98, Yao J17, Yousri NA99,100, Zhao W101, Adeyemo AA79, Afaq S19, Aguilar-Salinas CA102,103, Akiyama M3,104, Albert ML105,106,107,108, Allison MA109, Alver M110, Aung T111,112,113, Azizi F114, Bentley AR79, Boeing H115, Boerwinkle E116, Borja JB117, de Borst GJ118, Bottinger EP16,119, Broer L21, Campbell H1, Chanock S120, Chee ML111, Chen G79, Chen YI17, Chen Z11, Chiu YF121, Cocca M122, Collins FS123, Concas MP122, Corley J45,124, Cugliari G92, van Dam RM30,125,126, Damulina A47, Daneshpour MS127, Day FR12, Delgado GE56, Dhana K22,126,128, Doney ASF129, Dörr M130,131, Doumatey AP79, Dzimiri N132, Ebenesersdóttir SS5,133, Elliott J19, Elliott P19,40,134,135,136, Ewert R130, Felix JF22,23,137, Fischer K110, Freedman BI138, Girotto G8,139, Goel A58,140, Gögele M39, Goodarzi MO141, Graff M15, Granot-Hershkovitz E142, Grodstein F89, Guarrera S92, Gudbjartsson DF5,143, Guity K127, Gunnarsson B5, Guo Y144, Hagenaars SP45,124,145, Haiman CA146, Halevy A142, Harris TB86, Hedayati M127, van Heel DA147, Hirata M148, Höfer I149, Hsiung CA121, Huang J150, Hung YJ151,152, Ikram MA22, Jagadeesan A5,133, Jousilahti P153, Kamatani Y3,154, Kanai M2,3,155, Kerrison ND12, Kessler T156, Khaw KT157, Khor CC111,158, de Kleijn DPV118, Koh WP30,159, Kolcic I160, Kraft P126, Krämer BK56, Kutalik Z32,33, Kuusisto J161,162, Langenberg C12, Launer LJ86, Lawlor DA96,163,164, Lee IT165,166,167, Lee WJ168, Lerch MM169, Li L170, Liu J125,158, Loh M19,171,172, London SJ173, Loomis S174, Lu Y16, Luan J12, Mägi R110, Manichaikul AW175, Manunta P176, Másson G5, Matoba N3, Mei XW11, Meisinger C177, Meitinger T178,179,180, Mezzavilla M139, Milani L181, Millwood IY11, Momozawa Y182, Moore A120, Morange PE183,184, Moreno-Macías H185, Mori TA186, Morrison AC187, Muka T22,188, Murakami Y189, Murray AD190, de Mutsert R44, Mychaleckyj JC175, Nalls MA191,192, Nauck M131,193, Neville MJ194,195, Nolte IM65, Ong KK12,196, Orozco L197, 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Völker U53,131, Vuoksimaa E237, Wakil SM132, Waldenberger M27, Wander GS238, Wang YX239, Wareham NJ12, Wild S240, Yajnik CS241, Yuan JM242, Zeng L156, Zhang L111, Zhou J79, Amin N22, Asselbergs FW243,244,245,246, Bakker SJL247, Becker DM98, Lehne B19, Bennett DA248,249, van den Berg LH36, Berndt SI120, Bharadwaj D250, Bielak LF101, Bochud M32, Boehnke M217, Bouchard C251, Bradfield JP252,253, Brody JA254, Campbell A46, Carmi S142, Caulfield MJ94,95, Cesarini D255,256, Chambers JC19,20,40,257,258, Chandak GR74, Cheng CY111,112,113, Ciullo M70,212, Cornelis M259, Cusi D76,260,261, Smith GD96,164, Deary IJ45,124, Dorajoo R158, van Duijn CM11,22, Ellinghaus D262, Erdmann J66, Eriksson JG263,264,265,266,267, Evangelou E19,234, Evans MK86, Faul JD268, Feenstra B80, Feitosa M93, Foisy S269, Franke A262, Friedlander Y142, Gasparini P8,139, Gieger C27,61, Gonzalez C270, Goyette P269, Grant SFA35,252,271, Griffiths LR37, Groop L71,73, Gudnason V81,82, Gyllensten U55, Hakonarson H252,271, Hamsten A272, van der Harst P91, Heng CK273,274, Hicks AA39, Hochner H142, Huikuri H275, Hunt SC99,276, Jaddoe VWV22,23,137, De Jager PL277,278, Johannesson M279, Johansson Å55, Jonas JB239,280, Jukema JW87, Junttila J275, Kaprio J71,281, Kardia SLR101, Karpe F194,282, Kumari M25, Laakso M161,162, van der Laan SW283, Lahti J206,284, Laudes M285, Lea RA37, Lieb W286, Lumley T287, Martin NG43, März W56,288,289, Matullo G92, McCarthy MI58,194,282, Medland SE43, Merriman TR29, Metspalu A110, Meyer BF290, Mohlke KL83, Montgomery GW43,291, Mook-Kanamori D44,292, Munroe PB94,95, North KE15, Nyholt DR43,293, O'connell JR63,64, Ober C50, Oldehinkel AJ294, Palmas W295, Palmer C296, Pasterkamp GG149, Patin E203,204,205, Pennell CE297,298, Perusse L299,300, Peyser PA101, Pirastu M301, Polderman TJC51, Porteous DJ45,46, Posthuma D51,302, Psaty BM303,304, Rioux JD269,305, Rivadeneira F21,22,23, Rotimi C79, Rotter JI17, Rudan I1, Den Ruijter HM306, Sanghera DK78,307, Sattar N198, Schmidt R47, Schulze 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Nat Commun. 2019 Oct 31;10(1):4957.

doi: 10.1038/s41467-019-12283-6.

PMID: 31673082

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