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Algorithms
bioinformatics.....................................................158-161
DNA sequencing..............................................4,20,182
variant classification............................218,252,254,255
Annotation
conservation........................ ........................................253
DNA variant.................................................19,227,254
genome.................... ................................5,104,175,297
Association analysis
algorithm....................................................................3-4
genome wide association study...........................3,47, 71
single nucleotide polymorphism...................................71
Bayesian analysis.................................................90,160,176
Bioinformatics
algorithm....................................................158,251-261
analytic...................................................................17-29
bioinformatician............................................18, 41,189,
202,267
computational biology..................................................18
next-generation sequencing (NGS)............4,18, 84,189,
195-206
production..............................................................17-29
storage........................................................197,202-203
Cancer
germline....................................................87, 90, 92,210
somatic cell...................................................95,198,200
Chromosome microarray (CMA)
array comparative genomic hybridization
(aCGH)..........................................................122
array single nucleotide polymorphism........................122
balanced/unbalanced........................... 118,139,150,151
copy number variant (CNV).............118-125,128-137,
140,144-148,150-152
database......................................................119,128-133
de novo................................121,130,133,134,139,150
International Standards for Cytogenomics Analysis
(ISCA).............................119,125,133,145,152
loss of heterozygosity (LOH).....................127,138,151
quality control (QC)...........................................122,123
variant of unknown significance
(VOUS).................................. 129,131-135,145
Clinical annotation
cluster analysis...............................................34,40,167,
180,181
Comparative genomic hybridization CGH.
See Chromosome microarray (CMA) Computational biology. See Bioinformatics Computer aided drug designing
docking...............................................314,316,317,319 3-D protein structure..................................314, 315, 317
drug discovery.....................................313, 314, 317,319
drug-target interactions..............................................314
homology modeling............................................314-319
Copy number variant/alteration (CNV/CNA)............12,14,
19,25,92-93,118-125,128-137,140,144-148, 150-152,162-164,168
Database
browser.................................................. 8,128,133,175,
229,236,237,270,299
centralized..........................................................266,270
curation........................................Ill, 248,267,271,272
locus-specific......................................221,244,265,266
mutation...........................................8,22,215,221,255,
264-267
relational.............................................................264-266
standards.............................................................128,267
variant...........................................................13,263-272
Data imputation
genome wide association study (GWAS).....................76
single nucleotide polymorphism (SNP)..................76, 77
Data mining....................................................158,161,165,
166,168,176
Deletion
chromosome........................124,125,129,136,138,147
Diagnostics
comparative genomic hybridization (CGH)...............122
DNA (genetic) test.............................2,13, 66,200,228
Disease
complex............................................................7, 67,259
genetic..................................................18,212,215,267
Mendelian...........196,200,204,208,258,259,296,297
somatic........................................................198,200,210
Ronald Trent (ed.), Clinical Bioinformatics, Methods in Molecular Biology, vol. 1168, DOI 10.1007/978-1-4939-0847-9, © Springer Sclence+Business Media New York 2014
DNA
mutation...................................................83-89, 95,218
sequence
next-generation.....................................17-29, 83-96
reference.........................................4-5, 9,11,14-15
Sanger.........................................5, 9,13,27, 84,175,
205,224,227-249,298
targeted...............................................8-9,19, 87-88
variant.........................................209-214, 216,218-224,
227-249,252,255,260,263-272
Duplication
chromosome........................118,124,125,131,136-138
gene..............................................................92,119,136
Electronic medical record (EMR)
coding...........................................................................70
natural language processing..................................70,276
phenotype.........................................................66, 67, 70
Epistasis
biological......................................................................72
statistical.......................................................................72
Exome
next-generation sequencing.........................9,18,19,25,
87-89,196,218,220
orphan (rare) disease...........................................297,298
Filtering
DNA variant...............................................211,220,223
negative filtering...........................................................27
quality score..................................................................12
read trimming.........................................................23,24
variant call format.........................................................21
Gene
candidate.......................6, 8-9,13,15,54,221,295-310
discovery.............................................162,209,295-310
mapping...................................................2,3,5,8,14,15
mutation........................22,196, 215,244,245, 255,296
orphan (rare)...............................................295,298,299
Gene-gene interactions....................................162,168,245
Gene mapping
candidate................................................................6, 8-9
discovery.....................................................................2-3
next-generation sequencing................................4, 5, 8, 9
Gene prioritization (ranking)............296-301, 303, 309, 310
orphan (rare) disease...........................................298,299
Genome
algorithms...................................................................4, 7
NCBI.................................................. 110,130,179,231
reference sequence.....................21,24,26,178,231, 268
Genome-wide association study (GWAS)
case-control.....................................48, 49,54, 56, 58, 60
Hardy Weinberg equilibrium..................................52, 54
imputation..............................................................57-59
hnkage disequilibrium............................................55, 58
meta-analysis....................................................66, 75-76
minor allele frequency.............................................67-68
missing heritability...........................................66, 71-73
population stratification........................48, 53-56, 65, 71
principal component analysis (PCA)................54-56, 71
quality control (QC).............................51-53, 65, 73, 77
single nucleotide polymorphism......................48, 63, 65,
67-68,162
Genomic diagnosis
complex disease.......................................................83-96
incidental finding........................ 134,145,146, 207-224
next-generation sequencing (NGS)....................196-198
variant of unknown significance (VUS)......................228
Genomics...........................................13,18,19, 83-96,156,
162-165,168,175,177,190,199,222,237
genotype......................................138,142,143,146,150
H
High-throughput sequencing
targeted.........................................................8-9, 95,259
whole exome sequencing (WES).................8-10,19,21,
24,28,228,252,298
whole genome sequencing (WGS)....................8,10-15,
19,21,28, 87, 88, 93, 95,174,175,178,184, 189-191,196,209,228,252,259-260,296
Homology modeling........................................221, 314-319
comparative genomics.................................................315
I
Imputation
genome wide association study
(GWAS)...................................49,57-59, 76-77
genotype.............................................................7, 76-78
haplotype............................................................7, 76, 77
polymorphisms.............................................................57
Incidental finding
consent................................................................208,222
filtering...............................................210,211,216-223
inheritance..................................................211-212,219
phenotype...................................207-209,211, 212,221
risk......................................................208-215,219,223
variant database..................208-211,218-219, 221-222
Infectious disease. See Pathogen
Insertion deletion (indel)..................................3, 6, 9,12,13,
19,25,26,28, 89-92, 96,175,178,191,218,220, 224,259,298
In silico................95,107,121,216,222,228,230,233-242,
244-246,248,254,255,258,264, 313-315,319
In vitro........................187,189,233,244,245,253,264,265
In vivo............................32,38,187,232,244,245,253,320
Linkage disequilibrium (LD)........................5-7,55-58, 65,
66,68,73-77,212,252
single nucleotide polymorphism...............................6, 68
Loss of heterozygosity (LOH). See also Somatic mutation cancer..........................................................127,138,151
M
Machine learning method/algorithm
cross validation.......................................................38, 43
data set..................................................................37,176
statistical model............................................................37
supervised/unsupervised (clustering)..........................160
Mapping. See Gene mapping
Mass spectrometry (MS). See Metabolomics
Metabolites
Human Metabolome Database.....................................36
phenotype.............................................31,32, 34,48,49
profiling..................................................................31, 33
Metabolomics
analyte....................................................................36-40
liquid chromatography (LC)...................................33, 39
mass spectrometry (MS).........................................35, 36
nuclear magnetic resonance (NMR).............................36
targeted...................................................................32-39
untargeted...................................................34-36, 39-40
Microarray. See also Chromosome microarray (CMA)
comparative genomic hybridization (CGH)...............122
single nucleotide polymorphism (SNP)......................122
Microbial genomics. See Pathogen MicroRNA (miRNA)
miRBase.............................................107-109,111,112
miRNA target.....................................................110,115
non-coding RNA (ncRNA)..................99,100,104,106,
107,111,113
Missense variants. See Mutation detection; Variant Missing heritability
complex disease.......................................................64, 66
genome wide association study
(GWAS).........................................64,66, 71-73
Multiple testing....................................................49, 74,228
Mutation detection
animal model................................................................14
annotation.......................................................................5
comparative genomics.....................................................5
database..........................................................................7
family studies......................................................243-244
literature....................................................................271
pathogenic..........................................................245,271
pathogenicity prediction.............................................241
population frequency..................212-214,242-243,247
in silico.................................................95,228,233,258
variant of unknown significance (VUS)..............245,259
in vitro........................................................189,253,265
in vivo......................... ........................................187,253
N
Natural language processing (NLP)
architecture.........................................................275-292
biomedicine........................................................275-292
clinical decision support.....................................275,277
electronic medical record (EMR)...............276,288,292
knowledge resources...................276-279, 282-288,290
machine learning.........................276,279,280,290,291
tools............................................................276-281,290
unified medical language system.........................276,279
Next-generation sequencing (NGS)
bioinformatics (production, analytic, storage).........83-96
clinical vs. research applications..................................196
high throughput...............................................8, 84,198
massively parallel................................................195,197
quality measures............................................86,196,199
targeted gene sequencing........................................87-89
whole exome sequencing (WES)..............................9-10
whole genome sequencing (WGS).........................10-14
Omics
comparative........................ ........................................167
genomics.......................................................86,162-164
metabolomics..............................................................167
phenomics...................................................................158
proteomics..........................................................166-167
transcriptomics...................................................164-166
Orphan (rare) disease
biological networks.....................................................296
candidate gene....................................................295-310
locus............................................................................296
prioritization..................... ..................................295-310
Pathogen
bio-surveillance...........................................174,175,177
cluster..................................174-176,179-183,186-187
infectious disease.........................176,177,179,183,188
phylogenies.........................................176,179,181-183
public health....................................... 174,175,189,190
whole genome sequencing (WGS)............174,175,178,
184,189-191
Pathway
analysis..................................................41,158-167,169
data mining..................................158,161,165,166,168
discovery.............................................162,163,166,169
interactive...........................................................161,167
machine learning........................................160-161,168
Clinical Bioinformatics Index
Phenomics........................................................................158
Phenotype..................................1-15,31,32,34,48,49,59,
65-67, 69-70, 72-75, 77,118,119,130,132, 134,137,145-147,162,163,166-168,178, 207-209,211,212,221,222,228,242,243,245, 252,253,255,257,258,263,265-270,288,291, 296,297,299, 309
gene mapping..........................................2, 3,5, 8,14,15
Polymorphisms
restriction fragment length polymorphism
(RFLP).........................................................2,13
single nucleotide polymorphism (SNP).......2,48, 63, 65,
67-68,122,159,162,178
Population stratification........................48, 53-56, 60, 65, 71
genome wide association study (GWAS)...............47-60
Principal component analysis (PCA).....................54-56, 71,
183,188,192
Proteomics
biomarker discovery....................................158,166,169
p athway discovery.......................................................158
Public health surveillance. See Pathogen
Quality assurance
coverage...........................................................5,10, 202
reference genome..................................................3, 5,10
replication.....................................................................65
Quality control (QC)
filtering.......................................................22,23,65,73
validation....................................................................199
Rare disease. See Orphan disease
Sequencing. See Next-generation sequencing (NGS) Single nucleotide polymorphism (SNP)
annotation...........................................................239,240
association study...........................................63,162,164
dbSNP..................................13,22,26, 67, 87,213,229,
237,242-244,247,248,253,254,298
GWAS............................................................65,67,164
linkage disequilibrium.....................6,55, 65, 66, 68,212
population frequency..................................212,242-243
synonymous/non-synonymous.............................26,239
variant...................................................................10,239
Single nucleotide variation (SNV). See Single nucleotide
polymorphism (SNP) Somatic mutation
copy number alteration/variant (CN V/CNA)........92, 93
germline mutation........................................................89
heterogeneity............................................84, 85, 94,256
ploidy................................................................84-86, 94
structural rearrangement.............................84, 88, 92-94
tumor/cancer.......................84-87, 89, 94,200, 256,259
variant caller software.............................................88-90
Standards
quality analysis (QA)..........................................101-102
quality control (QC).................................19,22-24,127
statistical analysis..............................................34, 36-40
Structural rearrangements...............12,14, 84, 88, 89, 92-94
Supervised analysis. See Machine learning
System architecture..................................................275-292
Transcriptomics.
u
.158,164-169
Unified medical language system. See Natural language processing
Unsupervised analysis. See Machine learning
Variant. See also Single nucleotide polymorphism (SNP)
annotation...................................................228, 253,254
causal..................2,4, 6-9,11,13, 68,196,252,255,298
classification...............................................229, 245-247
database.......................................................13,214,218,
263-272
Variant of unknown significance (VUS/VOUS)
chromosome micro array.....................129,131-135,145
DNA variant/mutation...............................................228
genomic diagnosis.......................................................228
somatic mutation................................................245,259
w
Whole exome sequencing (WES).....................8,19,21,24,
28,208,298
Whole genome sequence(ing) (WGS)....................8,10-15,
18,21,28, 87, 93, 95,174,175,178,184,
189-191,196,209,228,252,259-260.
See also Next-generation sequencing (NGS)
