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: GAA: V816I

PubMed Link: 37012232

Variant Present in the following documents:

• 41467_2023_37547_MOESM12_ESM.xlsx, sheet 3
• 41467_2023_37547_MOESM12_ESM.xlsx, sheet 2

View BVdb publication page

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Expanding the prostate cancer cell line repertoire with ACRJ-PC28, an AR-negative neuroendocrine cell line derived from an African-Caribbean patient.

Cancer Research Communications

Valentine, Henkel H; Aiken, William W; Morrison, Belinda B; Zhao, Ziran Z; Fowle, Holly H; Wasserman, Jason S JS; Thompson, Elon E; Chin, Warren W; Young, Mark M; Clarke, Shannique S; Gibbs, Denise D; Harrison, Sharon S; McLaughlin, Wayne W; Kwok, Tim T; Jin, Fang F; Campbell, Kerry S KS; Horvath, Anelia A; Thompson, Rory R; Lee, Norman H NH; Zhou, Yan Y; Graña, Xavier X; Ragin, Camille C; Badal, Simone S

Publication Date: 2022-11

Variant appearance in text: GAA: V816I; rs1800314

PubMed Link: 36643868

Variant Present in the following documents:

• crc-22-0245-s07.xlsx, sheet 1

View BVdb publication page

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Current status of newborn screening for Pompe disease in Japan.

Orphanet Journal Of Rare Diseases

Sawada, Takaaki T; Kido, Jun J; Sugawara, Keishin K; Momosaki, Ken K; Yoshida, Shinichiro S; Kojima-Ishii, Kanako K; Inoue, Takahito T; Matsumoto, Shirou S; Endo, Fumio F; Ohga, Shouichi S; Hirose, Shinichi S; Nakamura, Kimitoshi K

Publication Date: 2021-12-18

Variant appearance in text: GAA: V816I; rs1800314

PubMed Link: 34922579

Variant Present in the following documents:

• Main text
• 13023_2021_Article_2146.pdf

View BVdb publication page

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Selective screening for lysosomal storage disorders in a large cohort of minorities of African descent shows high prevalence rates and novel variants.

Jimd Reports

Limgala, Renuka Pudi RP; Furtak, Vyacheslav V; Ivanova, Margarita M MM; Changsila, Erk E; Wilks, Floyd F; Fidelia-Lambert, Marie N MN; Goker-Alpan, Ozlem O; Gondré-Lewis, Marjorie C MC

Publication Date: 2021-05

Variant appearance in text: GAA: V816I

PubMed Link: 33977031

Variant Present in the following documents:

• Main text

View BVdb publication page

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Update of the Pompe variant database for the prediction of clinical phenotypes: Novel disease-associated variants, common sequence variants, and results from newborn screening.

Human Mutation

de Faria, Douglas O S DOS; 't Groen, Stijn L M In SLMI; Hoogeveen-Westerveld, Marianne M; Nino, Monica Y MY; van der Ploeg, Ans T AT; Bergsma, Atze J AJ; Pijnappel, W W M Pim WWMP

Publication Date: 2021-02

Variant appearance in text: GAA: 2446G>A; rs1800314

PubMed Link: 33560568

Variant Present in the following documents:

• Main text
• HUMU-42-119.pdf

View BVdb publication page

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Update of the Pompe variant database for the prediction of clinical phenotypes: Novel disease-associated variants, common sequence variants, and results from newborn screening.

Human Mutation

de Faria, Douglas O S DOS; 't Groen, Stijn L M In SLMI; Hoogeveen-Westerveld, Marianne M; Nino, Monica Y MY; van der Ploeg, Ans T AT; Bergsma, Atze J AJ; Pijnappel, W W M Pim WWMP

Publication Date: 2021-02

Variant appearance in text: GAA: 2446G>A; rs1800314

PubMed Link: 33560568

Variant Present in the following documents:

• Main text
• HUMU-42-119.pdf

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: GAA: V816I; rs1800314

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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Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy.

Cell

Krug, Karsten K; Jaehnig, Eric J EJ; Satpathy, Shankha S; Blumenberg, Lili L; Karpova, Alla A; Anurag, Meenakshi M; Miles, George G; Mertins, Philipp P; Geffen, Yifat Y; Tang, Lauren C LC; Heiman, David I DI; Cao, Song S; Maruvka, Yosef E YE; Lei, Jonathan T JT; Huang, Chen C; Kothadia, Ramani B RB; Colaprico, Antonio A; Birger, Chet C; Wang, Jarey J; Dou, Yongchao Y; Wen, Bo B; Shi, Zhiao Z; Liao, Yuxing Y; Wiznerowicz, Maciej M; Wyczalkowski, Matthew A MA; Chen, Xi Steven XS; Kennedy, Jacob J JJ; Paulovich, Amanda G AG; Thiagarajan, Mathangi M; Kinsinger, Christopher R CR; Hiltke, Tara T; Boja, Emily S ES; Mesri, Mehdi M; Robles, Ana I AI; Rodriguez, Henry H; Westbrook, Thomas F TF; Ding, Li L; Getz, Gad G; Clauser, Karl R KR; Fenyö, David D; Ruggles, Kelly V KV; Zhang, Bing B; Mani, D R DR; Carr, Steven A SA; Ellis, Matthew J MJ; Gillette, Michael A MA; ,

Publication Date: 2020-11-25

Variant appearance in text: GAA: V816I

PubMed Link: 33212010

Variant Present in the following documents:

• NIHMS1687926-supplement-Supplemental_Table_3.xlsx, sheet 5

View BVdb publication page

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Identification of pathogenic missense mutations using protein stability predictors.

Scientific Reports

Gerasimavicius, Lukas L; Liu, Xin X; Marsh, Joseph A JA

Publication Date: 2020-09-21

Variant appearance in text: GAA: V816I

PubMed Link: 32958805

Variant Present in the following documents:

• 41598_2020_72404_MOESM2_ESM.xlsx, sheet 3

View BVdb publication page

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Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis.

Nature Communications

Wen, Bo B; Li, Kai K; Zhang, Yun Y; Zhang, Bing B

Publication Date: 2020-04-09

Variant appearance in text: GAA: V816I

PubMed Link: 32273506

Variant Present in the following documents:

• 41467_2020_15456_MOESM4_ESM.xlsx, sheet 1
• 41467_2020_15456_MOESM6_ESM.xlsx, sheet 1

View BVdb publication page

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GAA compound heterozygous mutations associated with autophagic impairment cause cerebral infarction in Pompe disease.

Aging

Jia, Xiaodong X; Shao, Libin L; Liu, Chengcheng C; Chen, Tuanzhi T; Peng, Ling L; Cao, Yinguang Y; Zhang, Chuanchen C; Yang, Xiafeng X; Zhang, Guifeng G; Gao, Jianlu J; Fan, Guangyi G; Gu, Mingliang M; Du, Hongli H; Xia, Zhangyong Z

Publication Date: 2020-03-03

Variant appearance in text: GAA: 2446G>A

PubMed Link: 32126021

Variant Present in the following documents:

• Main text
• aging-12-102879.pdf

View BVdb publication page

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GAA variants and phenotypes among 1,079 patients with Pompe disease: Data from the Pompe Registry.

Human Mutation

Reuser, Arnold J J AJJ; van der Ploeg, Ans T AT; Chien, Yin-Hsiu YH; Llerena, Juan J; Abbott, Mary-Alice MA; Clemens, Paula R PR; Kimonis, Virginia E VE; Leslie, Nancy N; Maruti, Sonia S SS; Sanson, Bernd-Jan BJ; Araujo, Roberto R; Periquet, Magali M; Toscano, Antonio A; Kishnani, Priya S PS; On Behalf Of The Pompe Registry Sites,

Publication Date: 2019-11

Variant appearance in text: GAA: 2446G>A; Val816Ile

PubMed Link: 31342611

Variant Present in the following documents:

• HUMU-40-2146-s001.pdf

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: GAA: 2446G>A; Val816Ile

PubMed Link: 30937429

Variant Present in the following documents:

• famiglietti_supplementarytables1_rev_baz040.xlsx, sheet 1

View BVdb publication page

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Transcriptomic signature reveals mechanism of flower bud distortion in witches'-broom disease of soybean (Glycine max).

Bmc Plant Biology

Jaiswal, Sarika S; Jadhav, Pravin V PV; Jasrotia, Rahul Singh RS; Kale, Prashant B PB; Kad, Snehal K SK; Moharil, Mangesh P MP; Dudhare, Mahendra S MS; Kheni, Jashminkumar J; Deshmukh, Amit G AG; Mane, Shyamsundar S SS; Nandanwar, Ravindra S RS; Penna, Suprasanna S; Manjaya, Joy G JG; Iquebal, Mir Asif MA; Tomar, Rukam Singh RS; Kawar, Prashant G PG; Rai, Anil A; Kumar, Dinesh D

Publication Date: 2019-01-15

Variant appearance in text: GAA: 2446G>A; Val816Ile

PubMed Link: 30646861

Variant Present in the following documents:

• 12870_2018_1601_MOESM7_ESM.xlsx, sheet 1

View BVdb publication page

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Genetic Evidence Supporting the Role of the Calcium Channel, CACNA1S, in Tooth Cusp and Root Patterning.

Frontiers In Physiology

Laugel-Haushalter, Virginie V; Morkmued, Supawich S; Stoetzel, Corinne C; Geoffroy, Véronique V; Muller, Jean J; Boland, Anne A; Deleuze, Jean-François JF; Chennen, Kirsley K; Pitiphat, Waranuch W; Dollfus, Hélène H; Niederreither, Karen K; Bloch-Zupan, Agnès A; Pungchanchaikul, Patimaporn P

Publication Date: 2018

Variant appearance in text: GAA: 2446G>A; Val816Ile; rs1800314

PubMed Link: 30319441

Variant Present in the following documents:

• Table_6.xlsx, sheet 1
• Table_7.xlsx, sheet 1

View BVdb publication page

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A likely pathogenic variant putatively affecting splicing of PIGA identified in a multiple congenital anomalies hypotonia-seizures syndrome 2 (MCAHS2) family pedigree via whole-exome sequencing.

Molecular Genetics & Genomic Medicine

Yang, Junli J; Wang, Qiong Q; Zhuo, Qingcui Q; Tian, Huiling H; Li, Wen W; Luo, Fang F; Zhang, Jinghui J; Bi, Dan D; Peng, Jing J; Zhou, Dong D; Xin, Huawei H

Publication Date: 2018-09

Variant appearance in text: GAA: 2446G>A; V816I; rs1800314

PubMed Link: 29974678

Variant Present in the following documents:

• MGG3-6-739-s002.xlsx, sheet 6

View BVdb publication page

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Sources of discordance among germ-line variant classifications in ClinVar.

Genetics In Medicine : Official Journal Of The American College Of Medical Genetics

Yang, Shan S; Lincoln, Stephen E SE; Kobayashi, Yuya Y; Nykamp, Keith K; Nussbaum, Robert L RL; Topper, Scott S

Publication Date: 2017-10

Variant appearance in text: GAA: 2446G>A; Val816Ile

PubMed Link: 28569743

Variant Present in the following documents:

• gim201760x7.xlsx, sheet 2

View BVdb publication page

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Proteogenomics connects somatic mutations to signalling in breast cancer.

Nature

Mertins, Philipp P; Mani, D R DR; Ruggles, Kelly V KV; Gillette, Michael A MA; Clauser, Karl R KR; Wang, Pei P; Wang, Xianlong X; Qiao, Jana W JW; Cao, Song S; Petralia, Francesca F; Kawaler, Emily E; Mundt, Filip F; Krug, Karsten K; Tu, Zhidong Z; Lei, Jonathan T JT; Gatza, Michael L ML; Wilkerson, Matthew M; Perou, Charles M CM; Yellapantula, Venkata V; Huang, Kuan-lin KL; Lin, Chenwei C; McLellan, Michael D MD; Yan, Ping P; Davies, Sherri R SR; Townsend, R Reid RR; Skates, Steven J SJ; Wang, Jing J; Zhang, Bing B; Kinsinger, Christopher R CR; Mesri, Mehdi M; Rodriguez, Henry H; Ding, Li L; Paulovich, Amanda G AG; Fenyö, David D; Ellis, Matthew J MJ; Carr, Steven A SA; ,

Publication Date: 2016-06-02

Variant appearance in text: GAA: V816I; rs1800314

PubMed Link: 27251275

Variant Present in the following documents:

• NIHMS778057-supplement-supp_table5.xlsx, sheet 2

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: rs1800314

PubMed Link: 26659599

Variant Present in the following documents:

• pone.0144692.s002.xlsx, sheet 1

View BVdb publication page

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HERC5 is a prognostic biomarker for post-liver transplant recurrent human hepatocellular carcinoma.

Journal Of Translational Medicine

Xue, Feng F; Higgs, Brandon W BW; Huang, Jiaqi J; Morehouse, Chris C; Zhu, Wei W; Yao, Xin X; Brohawn, Philip P; Xiao, Zhan Z; Sebastian, Yinong Y; Liu, Zheng Z; Xia, Yun Y; Shen, Dong D; Kuziora, Mike M; Dong, Zhengwei Z; Han, Hulin H; Gu, Yi Y; Gu, Jianren J; Xia, Qiang Q; Yao, Yihong Y

Publication Date: 2015-12-11

Variant appearance in text: GAA: V816I; rs1800314

PubMed Link: 26653219

Variant Present in the following documents:

• 12967_2015_743_MOESM1_ESM.xlsx, sheet 5

View BVdb publication page

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GESPA: classifying nsSNPs to predict disease association.

Bmc Bioinformatics

Khurana, Jay K JK; Reeder, Jay E JE; Shrimpton, Antony E AE; Thakar, Juilee J

Publication Date: 2015-07-25

Variant appearance in text: GAA: V816I

PubMed Link: 26206375

Variant Present in the following documents:

• 12859_2015_673_MOESM1_ESM.xls, sheet 2

View BVdb publication page

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Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan.

Bmc Genomics

Ilyas, Muhammad M; Kim, Jong-Soo JS; Cooper, Jesse J; Shin, Young-Ah YA; Kim, Hak-Min HM; Cho, Yun Sung YS; Hwang, Seungwoo S; Kim, Hyunho H; Moon, Jaewoo J; Chung, Oksung O; Jun, JeHoon J; Rastogi, Achal A; Song, Sanghoon S; Ko, Junsu J; Manica, Andrea A; Rahman, Ziaur Z; Husnain, Tayyab T; Bhak, Jong J

Publication Date: 2015-03-12

Variant appearance in text: GAA: V816I; rs1800314

PubMed Link: 25887915

Variant Present in the following documents:

• 12864_2015_1290_MOESM7_ESM.xlsx, sheet 1

View BVdb publication page

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Clinical and GAA gene mutation analysis in mainland Chinese patients with late-onset Pompe disease: identifying c.2238G > C as the most common mutation.

Bmc Medical Genetics

Liu, Xiao X; Wang, Zhaoxia Z; Jin, Weina W; Lv, He H; Zhang, Wei W; Que, Chengli C; Huang, Yu Y; Yuan, Yun Y

Publication Date: 2014-12-20

Variant appearance in text: GAA: 2446G>A

PubMed Link: 25526786

Variant Present in the following documents:

• Main text
• 12881_2014_Article_141.pdf

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: GAA: V816I; rs1800314

PubMed Link: 25390934

Variant Present in the following documents:

• pone.0112430.s004.xlsx, sheet 1

View BVdb publication page

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NCI-60 whole exome sequencing and pharmacological CellMiner analyses.

Plos One

Reinhold, William C WC; Varma, Sudhir S; Sousa, Fabricio F; Sunshine, Margot M; Abaan, Ogan D OD; Davis, Sean R SR; Reinhold, Spencer W SW; Kohn, Kurt W KW; Morris, Joel J; Meltzer, Paul S PS; Doroshow, James H JH; Pommier, Yves Y

Publication Date: 2014

Variant appearance in text: GAA: V816I; rs1800314

PubMed Link: 25032700

Variant Present in the following documents:

• pone.0101670.s004.xlsx, sheet 1

View BVdb publication page

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A cross-sectional single-centre study on the spectrum of Pompe disease, German patients: molecular analysis of the GAA gene, manifestation and genotype-phenotype correlations.

Orphanet Journal Of Rare Diseases

Herzog, Andreas A; Hartung, Ralf R; Reuser, Arnold J J AJ; Hermanns, Pia P; Runz, Heiko H; Karabul, Nesrin N; Gökce, Seyfullah S; Pohlenz, Joachim J; Kampmann, Christoph C; Lampe, Christina C; Beck, Michael M; Mengel, Eugen E

Publication Date: 2012-06-07

Variant appearance in text: GAA: 2446G>A

PubMed Link: 22676651

Variant Present in the following documents:

• Main text
• 1750-1172-7-35.pdf

View BVdb publication page

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