abbreviations.tex

\chap{Abbreviations}

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\begin{longtabu}{lX}
ABiM       & All Breast Cancers in Malmö study \\
AIMS       & Absolute Intrinsic Molecular Subtypes \\
AJCC       & American Joint Committee on Cancer \\
ASR        & Age-standardized incidence rate \\
bp         & base pair \\
BAC        & bacterial artificial chromosome \\
BAM        & Binary alignment/map file format \\
BCS        & breast-conserving surgery \\
ctDNA      & Circulating tumor DNA \\
CNV        & Copy-number variant \\
CTC        & Circularing tumor cell \\
DCIS       & Ductal carcinoma \textit{in situ} \\
dNTP       & deoxyribonucleotide triphosphate; \texttt{A}, \texttt{T}, \texttt{G}, or \texttt{C} \\
ER         & Estrogen receptor \\
FDA        & Food and Drug Administration \\
ESMO       & European Society for Medical Oncology \\
FPKM       & Fragments per kilobase of exon per million mapped reads \\
GEO        & Gene expression omnibus \\
HER2       & Human epidermal growth factor receptor 2 \\
HoR        & Hormone receptor (ER and/or PgR) \\
HR         & Hazard ratio \\
HTS        & High-throughput sequencing, also called next-generation sequencing, deep sequencing, or massively parallel sequencing \\
indel      & Short insertion or deletion \\
IDC        & Invasive ductal carcinoma \\
IHC        & Immunohistochemistry \\
ILC        & Invasive lobular carcinoma \\
KM         & Kaplan-Meier \\
LoH        & Loss of Heterozygosity \\
mRNA       & messenger RNA \\
MAF        & Mutant allele frequency \\
Mb         & Megabase \\
MRD        & Minimal residual disease \\
NCBI       & National Center for Biotechnology Information \\
NHG        & Nottingham histological grade \\
NMD        & Nonsense-mediated decay \\
NMF        & Non-negative matrix factorization \\
OS         & Overall survival \\
PAM        & Prediction Analysis of Microarrays \\
PAM50      & Prediction Analysis of Microarrays 50 gene signature \\
PARP       & Poly (ADP-ribose) polymerase \\
PCR        & Polymerase chain-reaction \\
PgR        & Progesterone receptor \\
RNA-seq    & Illumina short-read cDNA sequencing \\
RPKM       & Reads per kilobase of exon per million mapped reads \\
\scanb{}   & Sweden Cancerome Analysis Network--Breast \\
SERD       & Selective estrogen receptor degrader \\
SNP        & Single nucleotide polymorphism \\
SNV        & Single nucleotide variant \\
SSP        & Single sample predictor \\
SV         & Structural variant \\
TCGA       & The Cancer Genome Atlas \\
TKI        & Tyrosine kinase inhibitor \\
TMB        & Tumor mutational burden \\
TNBC       & Triple-negative breast cancer \\
TNM        & TNM (tumor, node, metastasis) staging system \\
TPM        & Transcripts per million reads \\
TRK        & Tyrosine receptor kinase \\
UICC       & Union for International Cancer Control \\
VAF        & Variant allele frequency \\
WES        & Whole exome sequencing \\
WGS        & Whole genome sequencing \\
\end{longtabu}
}