Publications:

---

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: NPC1: R1266Q

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

---

Comprehensive proteogenomic characterization of early duodenal cancer reveals the carcinogenesis tracks of different subtypes.

Nature Communications

Li, Lingling L; Jiang, Dongxian D; Liu, Hui H; Guo, Chunmei C; Zhao, Rui R; Zhang, Qiao Q; Xu, Chen C; Qin, Zhaoyu Z; Feng, Jinwen J; Liu, Yang Y; Wang, Haixing H; Chen, Weijie W; Zhang, Xue X; Li, Bin B; Bai, Lin L; Tian, Sha S; Tan, Subei S; Yu, Zixiang Z; Chen, Lingli L; Huang, Jie J; Zhao, Jian-Yuan JY; Hou, Yingyong Y; Ding, Chen C

Publication Date: 2023-03-29

Variant appearance in text: NPC1: R1266Q; rs1805084

PubMed Link: 36991000

Variant Present in the following documents:

• 41467_2023_37221_MOESM5_ESM.xlsx, sheet 3

View BVdb publication page

---

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: rs1805084

PubMed Link: 36582804

Variant Present in the following documents:

• Table_6.xlsx, sheet 1

View BVdb publication page

---

Integrated longitudinal analysis of adult grade 4 diffuse gliomas with long-term relapse interval revealed upregulation of TGF-β signaling in recurrent tumors.

Neuro-Oncology

Kashani, Elham E; Schnidrig, Désirée D; Hashemi Gheinani, Ali A; Ninck, Martina Selina MS; Zens, Philipp P; Maragkou, Theoni T; Baumgartner, Ulrich U; Schucht, Philippe P; Rätsch, Gunnar G; Rubin, Mark A MA; Berezowska, Sabina S; Ng, Charlotte K Y CKY; Vassella, Erik E; ,

Publication Date: 2022-09-17

Variant appearance in text: NPC1: 3797G>A; Arg1266Gln; rs1805084

PubMed Link: 36124685

Variant Present in the following documents:

• noac220_suppl_supplementary_table_s3.xlsx, sheet 1

View BVdb publication page

---

SMAP is a pipeline for sample matching in proteogenomics.

Nature Communications

Li, Ling L; Niu, Mingming M; Erickson, Alyssa A; Luo, Jie J; Rowbotham, Kincaid K; Guo, Kai K; Huang, He H; Li, Yuxin Y; Jiang, Yi Y; Hur, Junguk J; Liu, Chunyu C; Peng, Junmin J; Wang, Xusheng X

Publication Date: 2022-02-08

Variant appearance in text: NPC1: R1266Q

PubMed Link: 35136070

Variant Present in the following documents:

• 41467_2022_28411_MOESM4_ESM.xlsx, sheet 1

View BVdb publication page

---

Identification and Classification of Rare Variants in NPC1 and NPC2 in Quebec.

Scientific Reports

Touma, Lahoud L; Labrecque, Marjorie M; Tetreault, Martine M; Duquette, Antoine A

Publication Date: 2021-05-14

Variant appearance in text: NPC1: R1266Q

PubMed Link: 33990640

Variant Present in the following documents:

• Main text
• 41598_2021_Article_89630.pdf

View BVdb publication page

---

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: NPC1: R1266Q; rs1805084

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

---

Identification of a nonsense mutation in TNNI3K associated with cardiac conduction disease.

Journal Of Clinical Laboratory Analysis

Liu, Jiang J; Liu, Da D; Li, Muzheng M; Wu, Keke K; Liu, Na N; Zhao, Chenyu C; Shi, Xiaoliu X; Liu, Qiming Q

Publication Date: 2020-09

Variant appearance in text: NPC1: R1266Q; rs1805084

PubMed Link: 32529721

Variant Present in the following documents:

• JCLA-34-e23418-s003.xls, sheet 1

View BVdb publication page

---

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: NPC1: R1266Q

PubMed Link: 32273506

Variant Present in the following documents:

• 41467_2020_15456_MOESM6_ESM.xlsx, sheet 1

View BVdb publication page

---

Next-generation sequencing identified novel Desmoplakin frame-shift variant in patients with Arrhythmogenic cardiomyopathy.

Bmc Cardiovascular Disorders

Lin, Xiaoping X; Ma, Yuankun Y; Cai, Zhejun Z; Wang, Qiyuan Q; Wang, Lihua L; Huo, Zhaoxia Z; Hu, Dan D; Wang, Jian'an J; Xiang, Meixiang M

Publication Date: 2020-02-11

Variant appearance in text: NPC1: 3797G>A; R1266Q; rs1805084

PubMed Link: 32046637

Variant Present in the following documents:

• 12872_2020_1369_MOESM1_ESM.xlsx, sheet 1

View BVdb publication page

---

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: NPC1: 3797G>A; Arg1266Gln; rs1805084

PubMed Link: 31640808

Variant Present in the following documents:

• 13059_2019_1838_MOESM3_ESM.xlsx, sheet 1

View BVdb publication page

---

Establishment and genomic characterization of gingivobuccal carcinoma cell lines with smokeless tobacco associated genetic alterations and oncogenic PIK3CA mutation.

Scientific Reports

Pansare, Kshama K; Gardi, Nilesh N; Kamat, Sayee S; Dange, Prerana P; Previn, Rahul R; Gera, Poonam P; Kowtal, Pradnya P; Amin, Kishore K; Sarin, Rajiv R

Publication Date: 2019-06-04

Variant appearance in text: NPC1: R1266Q; rs1805084

PubMed Link: 31164688

Variant Present in the following documents:

• 41598_2019_44143_MOESM2_ESM.xls, sheet 1

View BVdb publication page

---

Breast cancer quantitative proteome and proteogenomic landscape.

Nature Communications

Johansson, Henrik J HJ; Socciarelli, Fabio F; Vacanti, Nathaniel M NM; Haugen, Mads H MH; Zhu, Yafeng Y; Siavelis, Ioannis I; Fernandez-Woodbridge, Alejandro A; Aure, Miriam R MR; Sennblad, Bengt B; Vesterlund, Mattias M; Branca, Rui M RM; Orre, Lukas M LM; Huss, Mikael M; Fredlund, Erik E; Beraki, Elsa E; Garred, Øystein Ø; Boekel, Jorrit J; Sauer, Torill T; Zhao, Wei W; Nord, Silje S; Höglander, Elen K EK; Jans, Daniel C DC; Brismar, Hjalmar H; Haukaas, Tonje H TH; Bathen, Tone F TF; Schlichting, Ellen E; Naume, Bjørn B; , ; Luders, Torben T; Borgen, Elin E; Kristensen, Vessela N VN; Russnes, Hege G HG; Lingjærde, Ole Christian OC; Mills, Gordon B GB; Sahlberg, Kristine K KK; Børresen-Dale, Anne-Lise AL; Lehtiö, Janne J

Publication Date: 2019-04-08

Variant appearance in text: NPC1: 3797G>A; R1266Q; rs1805084

PubMed Link: 30962452

Variant Present in the following documents:

• 41467_2019_9018_MOESM8_ESM.xlsx, sheet 2

View BVdb publication page

---

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: NPC1: 3797G>A; Arg1266Gln

PubMed Link: 30937429

Variant Present in the following documents:

• famiglietti_supplementarytables1_rev_baz040.xlsx, sheet 1

View BVdb publication page

---

Identification of novel compound heterozygous SPG7 mutations-related hereditary spastic paraplegia in a Chinese family: a case report.

Bmc Neurology

Zhang, Xiaoqian X; Zhang, Lei L; Wu, Yanqing Y; Li, Gang G; Chen, Shengcai S; Xia, Yuanpeng Y; Li, Hongge H

Publication Date: 2018-11-29

Variant appearance in text: rs1805084

PubMed Link: 30497413

Variant Present in the following documents:

• 12883_2018_1199_MOESM5_ESM.xlsx, sheet 1

View BVdb publication page

---

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: NPC1: 3797G>A; R1266Q; rs1805084

PubMed Link: 29974678

Variant Present in the following documents:

• MGG3-6-739-s002.xlsx, sheet 7
• MGG3-6-739-s002.xlsx, sheet 4
• MGG3-6-739-s002.xlsx, sheet 5

View BVdb publication page

---

Whole-exome sequencing analysis of Waardenburg syndrome in a Chinese family.

Human Genome Variation

Chen, Dezhong D; Zhao, Na N; Wang, Jing J; Li, Zhuoyu Z; Wu, Changxin C; Fu, Jie J; Xiao, Han H

Publication Date: 2017

Variant appearance in text: rs1805084

PubMed Link: 28690861

Variant Present in the following documents:

• hgv201727-s1.xls, sheet 1

View BVdb publication page

---

Novel NPC1 mutations with different segregation in two related Greek patients with Niemann-Pick type C disease: molecular study in the extended pedigree and clinical correlations.

Bmc Medical Genetics

Bountouvi, Evangelia E; Papadopoulou, Anna A; Vanier, Marie T MT; Nyktari, Georgia G; Kanellakis, Spyridon S; Michelakakis, Helen H; Dinopoulos, Argyrios A

Publication Date: 2017-05-04

Variant appearance in text: NPC1: R1266Q; rs1805084

PubMed Link: 28472934

Variant Present in the following documents:

• Main text
• 12881_2017_Article_409.pdf

View BVdb publication page

---

Assessment of plasma chitotriosidase activity, CCL18/PARC concentration and NP-C suspicion index in the diagnosis of Niemann-Pick disease type C: a prospective observational study.

Journal Of Translational Medicine

De Castro-Orós, Isabel I; Irún, Pilar P; Cebolla, Jorge Javier JJ; Rodriguez-Sureda, Victor V; Mallén, Miguel M; Pueyo, María Jesús MJ; Mozas, Pilar P; Dominguez, Carmen C; Pocoví, Miguel M; ,

Publication Date: 2017-02-21

Variant appearance in text: NPC1: Arg1266Gln

PubMed Link: 28222799

Variant Present in the following documents:

• Main text
• 12967_2017_Article_1146.pdf

View BVdb publication page

---

An uncommon inheritance pattern in Niemann-Pick disease type C: identification of probable paternal germline mosaicism in a Mexican family.

Bmc Neurology

Cervera-Gaviria, Marivi M; Alcántara-Ortigoza, Miguel Angel MA; González-Del Angel, Ariadna A; Moyers-Pérez, Paola P; Legorreta-Ramírez, Blanca Gabriela Lizet BG; Barrera-Carmona, Nancy N; Cervera-Gaviria, Jaime J

Publication Date: 2016-08-22

Variant appearance in text: rs1805084

PubMed Link: 27549128

Variant Present in the following documents:

• Main text
• 12883_2016_Article_649.pdf

View BVdb publication page

---

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: NPC1: R1266Q; rs1805084

PubMed Link: 27251275

Variant Present in the following documents:

• NIHMS778057-supplement-supp_table5.xlsx, sheet 2

View BVdb publication page

---

Gpnmb Is a Potential Marker for the Visceral Pathology in Niemann-Pick Type C Disease.

Plos One

Marques, André R A AR; Gabriel, Tanit L TL; Aten, Jan J; van Roomen, Cindy P A A CP; Ottenhoff, Roelof R; Claessen, Nike N; Alfonso, Pilar P; Irún, Pilar P; Giraldo, Pilar P; Aerts, Johannes M F G JM; van Eijk, Marco M

Publication Date: 2016

Variant appearance in text: NPC1: Arg1266Gln; rs1805084

PubMed Link: 26771826

Variant Present in the following documents:

• pone.0147208.s002.xls, sheet 1

View BVdb publication page

---

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: NPC1: R1266Q; rs1805084

PubMed Link: 26659599

Variant Present in the following documents:

• pone.0144692.s002.xlsx, sheet 1

View BVdb publication page

---

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: NPC1: R1266Q

PubMed Link: 26206375

Variant Present in the following documents:

• 12859_2015_673_MOESM1_ESM.xls, sheet 4

View BVdb publication page

---

Differential Association of Niemann-Pick C1 Gene Polymorphisms with Maternal Prepregnancy Overweight and Gestational Diabetes.

Journal Of Diabetes And Obesity

Garver, William S WS; de la Torre, Lesley L; Brennan, Matthew C MC; Luo, Li L; Jelinek, David D; Castillo, Joseph J JJ; Meyre, David D; Orlando, Robert A RA; Heidenreich, Randall A RA; Rayburn, William F WF

Publication Date: 2015

Variant appearance in text: NPC1: R1266Q; rs1805084

PubMed Link: 26120596

Variant Present in the following documents:

• Main text

View BVdb publication page

---

Whole-exome sequencing of primary plasma cell leukemia discloses heterogeneous mutational patterns.

Oncotarget

Cifola, Ingrid I; Lionetti, Marta M; Pinatel, Eva E; Todoerti, Katia K; Mangano, Eleonora E; Pietrelli, Alessandro A; Fabris, Sonia S; Mosca, Laura L; Simeon, Vittorio V; Petrucci, Maria Teresa MT; Morabito, Fortunato F; Offidani, Massimo M; Di Raimondo, Francesco F; Falcone, Antonietta A; Caravita, Tommaso T; Battaglia, Cristina C; De Bellis, Gianluca G; Palumbo, Antonio A; Musto, Pellegrino P; Neri, Antonino A

Publication Date: 2015-07-10

Variant appearance in text: NPC1: R1266Q; rs1805084

PubMed Link: 26046463

Variant Present in the following documents:

• oncotarget-06-17543-s002.xls, sheet 1

View BVdb publication page

---

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: NPC1: R1266Q; rs1805084

PubMed Link: 25773295

Variant Present in the following documents:

• srep09124-s3.xls, sheet 1

View BVdb publication page

---

High incidence of unrecognized visceral/neurological late-onset Niemann-Pick disease, type C1, predicted by analysis of massively parallel sequencing data sets.

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

Wassif, Christopher A CA; Cross, Joanna L JL; Iben, James J; Sanchez-Pulido, Luis L; Cougnoux, Antony A; Platt, Frances M FM; Ory, Daniel S DS; Ponting, Chris P CP; Bailey-Wilson, Joan E JE; Biesecker, Leslie G LG; Porter, Forbes D FD

Publication Date: 2016-01

Variant appearance in text: NPC1: 3797G>A; R1266Q; rs1805084

PubMed Link: 25764212

Variant Present in the following documents:

• Main text
• emss-62276.pdf

View BVdb publication page

---

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: NPC1: R1266Q; rs1805084

PubMed Link: 25390934

Variant Present in the following documents:

• pone.0112430.s004.xlsx, sheet 1

View BVdb publication page

---

Exome sequencing is an efficient tool for variant late-infantile neuronal ceroid lipofuscinosis molecular diagnosis.

Plos One

Patiño, Liliana Catherine LC; Battu, Rajani R; Ortega-Recalde, Oscar O; Nallathambi, Jeyabalan J; Anandula, Venkata Ramana VR; Renukaradhya, Umashankar U; Laissue, Paul P

Publication Date: 2014

Variant appearance in text: NPC1: Arg1266Gln

PubMed Link: 25333361

Variant Present in the following documents:

• pone.0109576.s001.xls, sheet 3
• pone.0109576.s003.xls, sheet 3
• pone.0109576.s002.xls, sheet 3

View BVdb publication page

---

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: NPC1: R1266Q; rs1805084

PubMed Link: 25032700

Variant Present in the following documents:

• pone.0101670.s004.xlsx, sheet 1

View BVdb publication page

---

Mammalian NPC1 genes may undergo positive selection and human polymorphisms associate with type 2 diabetes.

Bmc Medicine

Al-Daghri, Nasser M NM; Cagliani, Rachele R; Forni, Diego D; Alokail, Majed S MS; Pozzoli, Uberto U; Alkharfy, Khalid M KM; Sabico, Shaun S; Clerici, Mario M; Sironi, Manuela M

Publication Date: 2012-11-15

Variant appearance in text: NPC1: Arg1266Gln

PubMed Link: 23153210

Variant Present in the following documents:

• 1741-7015-10-140.pdf

View BVdb publication page

---

The National Niemann-Pick Type C1 Disease Database: correlation of lipid profiles, mutations, and biochemical phenotypes.

Journal Of Lipid Research

Garver, William S WS; Jelinek, David D; Meaney, F John FJ; Flynn, James J; Pettit, Kathleen M KM; Shepherd, Glen G; Heidenreich, Randall A RA; Vockley, Cate M Walsh CM; Castro, Graciela G; Francis, Gordon A GA

Publication Date: 2010-02

Variant appearance in text: NPC1: R1266Q

PubMed Link: 19744920

Variant Present in the following documents:

• Main text

View BVdb publication page

---