Publications:

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Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues.

Nature Communications

Abelin, Jennifer G JG; Bergstrom, Erik J EJ; Rivera, Keith D KD; Taylor, Hannah B HB; Klaeger, Susan S; Xu, Charles C; Verzani, Eva K EK; Jackson White, C C; Woldemichael, Hilina B HB; Virshup, Maya M; Olive, Meagan E ME; Maynard, Myranda M; Vartany, Stephanie A SA; Allen, Joseph D JD; Phulphagar, Kshiti K; Harry Kane, M M; Rachimi, Suzanna S; Mani, D R DR; Gillette, Michael A MA; Satpathy, Shankha S; Clauser, Karl R KR; Udeshi, Namrata D ND; Carr, Steven A SA

Publication Date: 2023-04-03

Variant appearance in text: PKD1: I4045V

PubMed Link: 37012232

Variant Present in the following documents:

• 41467_2023_37547_MOESM12_ESM.xlsx, sheet 2

View BVdb publication page

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Circulating messenger RNA variants as a potential biomarker for surveillance of hepatocellular carcinoma.

Frontiers In Oncology

Block, Timothy T; Zezulinski, Daniel D; Kaplan, David E DE; Lu, Jingqiao J; Zanine, Samantha S; Zhan, Tingting T; Doria, Cataldo C; Sayeed, Aejaz A

Publication Date: 2022

Variant appearance in text: rs10960

PubMed Link: 36582804

Variant Present in the following documents:

• Table_6.xlsx, sheet 1

View BVdb publication page

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Establishment and characterization of a new mantle cell lymphoma cell line with a NOTCH2 mutation, Arbo.

Ejhaem

Safa, Firas F; Rasmussen, Terri T; Lobelle-Rich, Patricia P; Collier, Stephanie S; Milligan, Nicholas N; Schmeig, John J; Schmid, Janet J; Wiewiorowski, Carol C; Totaro, Denise D; Brown, Theresa C TC; Satyavarapu, Ishwarya I; Badoo, Melody M; Ungerleider, Nathan N; Flemington, Erik K EK; Safah, Hana H; Saba, Nakhle S NS

Publication Date: 2022-11

Variant appearance in text: PKD1: I4045V; rs10960

PubMed Link: 36467812

Variant Present in the following documents:

• JHA2-3-1326-s001.xlsx, sheet 1

View BVdb publication page

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A genomic deletion encompassing CRYBB2-CRYBB2P1 is responsible for autosomal recessive congenital cataracts.

Human Genome Variation

Irum, Bushra B; Kabir, Firoz F; Shoshany, Nadav N; Khan, Shahid Y SY; Rauf, Bushra B; Naeem, Muhammad Asif MA; Qaiser, Tanveer A TA; Riazuddin, Sheikh S; Hejtmancik, J Fielding JF; Riazuddin, S Amer SA

Publication Date: 2022-09-08

Variant appearance in text: rs10960

PubMed Link: 36075891

Variant Present in the following documents:

• 41439_2022_208_MOESM4_ESM.xlsx, sheet 2
• 41439_2022_208_MOESM3_ESM.xlsx, sheet 2
• 41439_2022_208_MOESM5_ESM.xlsx, sheet 2

View BVdb publication page

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Genetic analysis of sinonasal undifferentiated carcinoma discovers recurrent SWI/SNF alterations and a novel PGAP3-SRPK1 fusion gene.

Bmc Cancer

Heft Neal, Molly E ME; Birkeland, Andrew C AC; Bhangale, Apurva D AD; Zhai, Jingyi J; Kulkarni, Aditi A; Foltin, Susan K SK; Jewell, Brittany M BM; Ludwig, Megan L ML; Pinatti, Lisa L; Jiang, Hui H; McHugh, Jonathan B JB; Marentette, Lawence L; McKean, Erin L EL; Brenner, J Chad JC

Publication Date: 2021-05-29

Variant appearance in text: PKD1: 12133A>G; Ile4045Val; rs10960

PubMed Link: 34051734

Variant Present in the following documents:

• 12885_2021_8370_MOESM15_ESM.xlsx, sheet 1

View BVdb publication page

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Integrated genetic and metabolic landscapes predict vulnerabilities of temozolomide resistant glioblastoma cells.

Npj Systems Biology And Applications

Immanuel, Selva Rupa Christinal SRC; Ghanate, Avinash D AD; Parmar, Dharmeshkumar S DS; Yadav, Ritu R; Uthup, Riya R; Panchagnula, Venkateswarlu V; Raghunathan, Anu A

Publication Date: 2021-01-08

Variant appearance in text: PKD1: I4045V; rs10960

PubMed Link: 33420045

Variant Present in the following documents:

• 41540_2020_161_MOESM3_ESM.xlsx, sheet 4
• 41540_2020_161_MOESM3_ESM.xlsx, sheet 3
• 41540_2020_161_MOESM3_ESM.xlsx, sheet 2

View BVdb publication page

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Identification of missense and synonymous variants in Iranian patients suffering from autosomal dominant polycystic kidney disease.

Bmc Nephrology

Khadangi, Fatemeh F; Torkamanzehi, Adam A; Kerachian, Mohammad Amin MA

Publication Date: 2020-09-21

Variant appearance in text: PKD1: Ile4045Val; rs10960

PubMed Link: 32957937

Variant Present in the following documents:

• Main text
• 12882_2020_Article_2069.pdf

View BVdb publication page

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The role of myoglobin in epithelial cancers: Insights from transcriptomics.

International Journal Of Molecular Medicine

Bicker, Anne A; Nauth, Theresa T; Gerst, Daniela D; Aboouf, Mostafa Ahmed MA; Fandrey, Joachim J; Kristiansen, Glen G; Gorr, Thomas Alexander TA; Hankeln, Thomas T

Publication Date: 2020-02

Variant appearance in text: PKD1: 12133A>G; Ile4045Val

PubMed Link: 31894249

Variant Present in the following documents:

• Supplementary_Data2.xlsx, sheet 1
• Supplementary_Data2.xlsx, sheet 2
• Supplementary_Data2.xlsx, sheet 8
• Supplementary_Data2.xlsx, sheet 3
• Supplementary_Data2.xlsx, sheet 7

View BVdb publication page

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Refinement of evolutionary medicine predictions based on clinical evidence for the manifestations of Mendelian diseases.

Scientific Reports

Šimčíková, Daniela D; Heneberg, Petr P

Publication Date: 2019-12-09

Variant appearance in text: PKD1: 12133A>G; I4045V

PubMed Link: 31819097

Variant Present in the following documents:

• 41598_2019_54976_MOESM2_ESM.xlsx, sheet 9

View BVdb publication page

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PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations.

Genome Biology

Zhang, Chao C; Gao, Yang Y; Ning, Zhilin Z; Lu, Yan Y; Zhang, Xiaoxi X; Liu, Jiaojiao J; Xie, Bo B; Xue, Zhe Z; Wang, Xiaoji X; Yuan, Kai K; Ge, Xueling X; Pan, Yuwen Y; Liu, Chang C; Tian, Lei L; Wang, Yuchen Y; Lu, Dongsheng D; Hoh, Boon-Peng BP; Xu, Shuhua S

Publication Date: 2019-10-22

Variant appearance in text: PKD1: 12133A>G; Ile4045Val; rs10960

PubMed Link: 31640808

Variant Present in the following documents:

• 13059_2019_1838_MOESM3_ESM.xlsx, sheet 1

View BVdb publication page

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Distinctive mutational spectrum and karyotype disruption in long-term cisplatin-treated urothelial carcinoma cell lines.

Scientific Reports

Skowron, Margaretha A MA; Petzsch, Patrick P; Hardt, Karin K; Wagner, Nicholas N; Beier, Manfred M; Stepanow, Stefanie S; Drechsler, Matthias M; Rieder, Harald H; Köhrer, Karl K; Niegisch, Günter G; Hoffmann, Michèle J MJ; Schulz, Wolfgang A WA

Publication Date: 2019-10-09

Variant appearance in text: PKD1: I4045V; rs10960

PubMed Link: 31597922

Variant Present in the following documents:

• 41598_2019_50891_MOESM2_ESM.xlsx, sheet 1
• 41598_2019_50891_MOESM3_ESM.xlsx, sheet 1

View BVdb publication page

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An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar.

Database : The Journal Of Biological Databases And Curation

Famiglietti, M L ML; Estreicher, A A; Breuza, L L; Poux, S S; Redaschi, N N; Xenarios, I I; Bridge, A A; ,

Publication Date: 2019-01-01

Variant appearance in text: PKD1: 12133A>G; Ile4045Val

PubMed Link: 30937429

Variant Present in the following documents:

• famiglietti_supplementarytables1_rev_baz040.xlsx, sheet 1

View BVdb publication page

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A reference collection of patient-derived cell line and xenograft models of proneural, classical and mesenchymal glioblastoma.

Scientific Reports

Stringer, Brett W BW; Day, Bryan W BW; D'Souza, Rochelle C J RCJ; Jamieson, Paul R PR; Ensbey, Kathleen S KS; Bruce, Zara C ZC; Lim, Yi Chieh YC; Goasdoué, Kate K; Offenhäuser, Carolin C; Akgül, Seçkin S; Allan, Suzanne S; Robertson, Thomas T; Lucas, Peter P; Tollesson, Gert G; Campbell, Scott S; Winter, Craig C; Do, Hongdo H; Dobrovic, Alexander A; Inglis, Po-Ling PL; Jeffree, Rosalind L RL; Johns, Terrance G TG; Boyd, Andrew W AW

Publication Date: 2019-03-20

Variant appearance in text: rs10960

PubMed Link: 30894629

Variant Present in the following documents:

• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 4
• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 6
• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 13
• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 10

View BVdb publication page

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PKD1 Duplicated regions limit clinical Utility of Whole Exome Sequencing for Genetic Diagnosis of Autosomal Dominant Polycystic Kidney Disease.

Scientific Reports

Ali, Hamad H; Al-Mulla, Fahd F; Hussain, Naser N; Naim, Medhat M; Asbeutah, Akram M AM; AlSahow, Ali A; Abu-Farha, Mohamed M; Abubaker, Jehad J; Al Madhoun, Ashraf A; Ahmad, Sajjad S; Harris, Peter C PC

Publication Date: 2019-03-11

Variant appearance in text: PKD1: 12133A>G; Ile4045Val; rs10960

PubMed Link: 30858458

Variant Present in the following documents:

• Main text
• 41598_2019_Article_40761.pdf

View BVdb publication page

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Organoids as a new model for improving regenerative medicine and cancer personalized therapy in renal diseases.

Cell Death & Disease

Grassi, Ludovica L; Alfonsi, Romina R; Francescangeli, Federica F; Signore, Michele M; De Angelis, Maria Laura ML; Addario, Antonio A; Costantini, Manuela M; Flex, Elisabetta E; Ciolfi, Andrea A; Pizzi, Simone S; Bruselles, Alessandro A; Pallocca, Matteo M; Simone, Giuseppe G; Haoui, Mustapha M; Falchi, Mario M; Milella, Michele M; Sentinelli, Steno S; Di Matteo, Paola P; Stellacci, Emilia E; Gallucci, Michele M; Muto, Giovanni G; Tartaglia, Marco M; De Maria, Ruggero R; Bonci, Désirée D

Publication Date: 2019-02-27

Variant appearance in text: PKD1: 12133A>G; rs10960

PubMed Link: 30814510

Variant Present in the following documents:

• 41419_2019_1453_MOESM27_ESM.xlsx, sheet 3

View BVdb publication page

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Identification of 613 new loci associated with heel bone mineral density and a polygenic risk score for bone mineral density, osteoporosis and fracture.

Plos One

Kim, Stuart K SK

Publication Date: 2018

Variant appearance in text: PKD1: I4045V; rs10960

PubMed Link: 30048462

Variant Present in the following documents:

• pone.0200785.s003.xlsx, sheet 1

View BVdb publication page

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Detecting PKD1 variants in polycystic kidney disease patients by single-molecule long-read sequencing.

Human Mutation

Borràs, Daniel M DM; Vossen, Rolf H A M RHAM; Liem, Michael M; Buermans, Henk P J HPJ; Dauwerse, Hans H; van Heusden, Dave D; Gansevoort, Ron T RT; den Dunnen, Johan T JT; Janssen, Bart B; Peters, Dorien J M DJM; Losekoot, Monique M; Anvar, Seyed Yahya SY

Publication Date: 2017-07

Variant appearance in text: PKD1: 12133A>G; Ile4045Val; rs10960

PubMed Link: 28378423

Variant Present in the following documents:

• HUMU-38-870-s001.pdf

View BVdb publication page

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Deciphering Variability of PKD1 and PKD2 in an Italian Cohort of 643 Patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD).

Scientific Reports

Carrera, Paola P; Calzavara, Silvia S; Magistroni, Riccardo R; den Dunnen, Johan T JT; Rigo, Francesca F; Stenirri, Stefania S; Testa, Francesca F; Messa, Piergiorgio P; Cerutti, Roberta R; Scolari, Francesco F; Izzi, Claudia C; Edefonti, Alberto A; Negrisolo, Susanna S; Benetti, Elisa E; Alibrandi, Maria Teresa Sciarrone MT; Manunta, Paolo P; Boletta, Alessandra A; Ferrari, Maurizio M

Publication Date: 2016-08-08

Variant appearance in text: rs10960

PubMed Link: 27499327

Variant Present in the following documents:

• srep30850-s2.xlsx, sheet 1

View BVdb publication page

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Deleterious coding variants in multi-case families with non-syndromic cleft lip and/or palate phenotypes.

Scientific Reports

Pengelly, Reuben J RJ; Arias, Liliana L; Martínez, Julio J; Upstill-Goddard, Rosanna R; Seaby, Eleanor G EG; Gibson, Jane J; Ennis, Sarah S; Collins, Andrew A; Briceño, Ignacio I

Publication Date: 2016-07-26

Variant appearance in text: PKD1: I4045V; rs10960

PubMed Link: 27456059

Variant Present in the following documents:

• srep30457-s2.xls, sheet 2
• srep30457-s2.xls, sheet 1

View BVdb publication page

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Clonal relationships between lobular carcinoma in situ and other breast malignancies.

Breast Cancer Research : Bcr

Begg, Colin B CB; Ostrovnaya, Irina I; Carniello, Jose V Scarpa JV; Sakr, Rita A RA; Giri, Dilip D; Towers, Russell R; Schizas, Michail M; De Brot, Marina M; Andrade, Victor P VP; Mauguen, Audrey A; Seshan, Venkatraman E VE; King, Tari A TA

Publication Date: 2016-06-23

Variant appearance in text: PKD1: I4045V

PubMed Link: 27334989

Variant Present in the following documents:

• 13058_2016_727_MOESM3_ESM.xlsx, sheet 1

View BVdb publication page

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Reproducible Analysis of Post-Translational Modifications in Proteomes--Application to Human Mutations.

Plos One

Holehouse, Alex S AS; Naegle, Kristen M KM

Publication Date: 2015

Variant appearance in text: PKD1: I4045V; rs10960

PubMed Link: 26659599

Variant Present in the following documents:

• pone.0144692.s002.xlsx, sheet 1

View BVdb publication page

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Generation of a High Number of Healthy Erythroid Cells from Gene-Edited Pyruvate Kinase Deficiency Patient-Specific Induced Pluripotent Stem Cells.

Stem Cell Reports

Garate, Zita Z; Quintana-Bustamante, Oscar O; Crane, Ana M AM; Olivier, Emmanuel E; Poirot, Laurent L; Galetto, Roman R; Kosinski, Penelope P; Hill, Collin C; Kung, Charles C; Agirre, Xabi X; Orman, Israel I; Cerrato, Laura L; Alberquilla, Omaira O; Rodriguez-Fornes, Fatima F; Fusaki, Noemi N; Garcia-Sanchez, Felix F; Maia, Tabita M TM; Ribeiro, Maria L ML; Sevilla, Julian J; Prosper, Felipe F; Jin, Shengfang S; Mountford, Joanne J; Guenechea, Guillermo G; Gouble, Agnes A; Bueren, Juan A JA; Davis, Brian R BR; Segovia, Jose C JC

Publication Date: 2015-12-08

Variant appearance in text: PKD1: I4045V; rs10960

PubMed Link: 26549847

Variant Present in the following documents:

• mmc3.xlsx, sheet 3
• mmc3.xlsx, sheet 2
• mmc3.xlsx, sheet 1

View BVdb publication page

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Exome sequencing of case-unaffected-parents trios reveals recessive and de novo genetic variants in sporadic ALS.

Scientific Reports

Steinberg, Karyn Meltz KM; Yu, Bing B; Koboldt, Daniel C DC; Mardis, Elaine R ER; Pamphlett, Roger R

Publication Date: 2015-03-16

Variant appearance in text: rs10960

PubMed Link: 25773295

Variant Present in the following documents:

• srep09124-s3.xls, sheet 1

View BVdb publication page

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Whole-genome sequencing of the world's oldest people.

Plos One

Gierman, Hinco J HJ; Fortney, Kristen K; Roach, Jared C JC; Coles, Natalie S NS; Li, Hong H; Glusman, Gustavo G; Markov, Glenn J GJ; Smith, Justin D JD; Hood, Leroy L; Coles, L Stephen LS; Kim, Stuart K SK

Publication Date: 2014

Variant appearance in text: PKD1: I4045V; rs10960

PubMed Link: 25390934

Variant Present in the following documents:

• pone.0112430.s004.xlsx, sheet 1

View BVdb publication page

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Molecular diagnosis of autosomal dominant polycystic kidney disease using next-generation sequencing.

The Journal Of Molecular Diagnostics : Jmd

Tan, Adrian Y AY; Michaeel, Alber A; Liu, Genyan G; Elemento, Olivier O; Blumenfeld, Jon J; Donahue, Stephanie S; Parker, Tom T; Levine, Daniel D; Rennert, Hanna H

Publication Date: 2014-03

Variant appearance in text: rs10960

PubMed Link: 24374109

Variant Present in the following documents:

• Main text

View BVdb publication page

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Evidence of a third ADPKD locus is not supported by re-analysis of designated PKD3 families.

Kidney International

Paul, Binu M BM; Consugar, Mark B MB; Ryan Lee, Moonnoh M; Sundsbak, Jamie L JL; Heyer, Christina M CM; Rossetti, Sandro S; Kubly, Vickie J VJ; Hopp, Katharina K; Torres, Vicente E VE; Coto, Eliecer E; Clementi, Maurizio M; Bogdanova, Nadja N; de Almeida, Edgar E; Bichet, Daniel G DG; Harris, Peter C PC

Publication Date: 2014-02

Variant appearance in text: PKD1: I4045V

PubMed Link: 23760289

Variant Present in the following documents:

• Main text
• nihms-481064.pdf

View BVdb publication page

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A novel long-range PCR sequencing method for genetic analysis of the entire PKD1 gene.

The Journal Of Molecular Diagnostics : Jmd

Tan, Ying-Cai YC; Michaeel, Alber A; Blumenfeld, Jon J; Donahue, Stephanie S; Parker, Tom T; Levine, Daniel D; Rennert, Hanna H

Publication Date: 2012-07

Variant appearance in text: PKD1: 12133A>G; I4045V; rs10960

PubMed Link: 22608885

Variant Present in the following documents:

• Main text

View BVdb publication page

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HSPVdb--the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands.

Immunogenetics

Nijveen, Harm H; Kester, Michel G D MG; Hassan, Chopie C; Viars, Aurélie A; de Ru, Arnoud H AH; de Jager, Machiel M; Falkenburg, J H Fred JH; Leunissen, Jack A M JA; van Veelen, Peter A PA

Publication Date: 2011-03

Variant appearance in text: rs10960

PubMed Link: 21125265

Variant Present in the following documents:

• Main text
• 251_2010_Article_497.pdf

View BVdb publication page

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New mutations in the PKD1 gene in Czech population with autosomal dominant polycystic kidney disease.

Bmc Medical Genetics

Stekrova, Jitka J; Reiterova, Jana J; Svobodova, Stanislava S; Kebrdlova, Vera V; Lnenicka, Petr P; Merta, Miroslav M; Viklicky, Ondrej O; Kohoutova, Milada M

Publication Date: 2009-08-17

Variant appearance in text: PKD1: 12133A>G; I4045V

PubMed Link: 19686598

Variant Present in the following documents:

• Main text
• 1471-2350-10-78.pdf

View BVdb publication page

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