Getting you ready for the course
GlossaryWe have included some key terms you will come across over the next five weeks that may need some further explanation or you would just like to know more about.The glossary and acronyms below will appear as links in the course pages so you can look back whenever you come across anything you’re not sure about. Here is a version of the glossary in pdf format so you can download it and keep it for future reference.A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
ADAutosomal Dominant (AD) describes inheritance pattern of a genetic condition where one copy of the variant gene is inherited from one of the parients.
ARAutosomal Recessive (AR) describes inheritance pattern of a genetic condition where two copies of the variant gene are inherited (one from each parent).
BioinformaticianPipelineBioinformatics pipeline also sometimes known as a workflow describes the set of steps required to convert the raw signal indicating a base pair, through to piecing the genome back together again and assigning where there are sequence variations in comparison to a reference genome.
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Clinical Bioinformatics: Unlocking Genomics in Healthcare
CloudCloud computing is the practice of using a network of remote servers to store, manage, and process data.
Codonis a set of 3 bases within the mRNA that encodes for a particular amino acid
CompoundHeterozygousCompound Heterozygous is where an individual has two different recessive alleles at a specific gene locus, one on each identical chromosome.back to the top
DeNovoDe novo mutations are when genetic variant occur in an offspring but are not present in either parent.back to the top
ESCEvolutionary Sequence Conservation (ESC) is where sequence similarity is used as evidence of structural and functional conservation, and evolutionary relationships between sequences.
ExACExome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects.
ExomeIs the part of the genome resulting from exons that code for proteins and functional RNAs.
ExonThe genome consists of introns, non-coding areas and exons, parts of the genome that can code for proteins or functional RNA molecules.back to the top
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GenePanelsSets of 10-100s of genes used to identify variants in the human genome linking to specific phenotypes or conditions.
GenotypeGenotype, at its broadest sense, is the genetic characteristics of an individual. When referring to a particular trait it describes the variant forms of a gene that are carried by an organism.
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IFIncidental Finding – unexpected genetic changes found during sequencing of the genome.
inSilicoPerform using computer modelling or simulation.back to the top
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LinuxComputer operating system.
LSBDLocus specific Database (LSBD): A database describing variants found at particular gene loci.back to the top
MicrobiologyThe branch of science that deals with micro-organisms.
Mis-senseA Mis-sense is a single base pair change that will cause the formation of an alternate amino acid at that position in the sequence.
MSAMultiple Sequence Alignment is generally the alignment of two three or more biological sequences (protein or nucleic acid) of similar length. From the output of the alignments, homology can be inferred and the evolutionary relationships between the sequences studied.back to the top
NGSNext Generation Sequencing (NGS) – the process by which millions of fragments of DNA can be sequenced in parallel from the same sample.
NonsenseMediatedDecayIn cases where a premature stop codon is incorporated into the mRNA a truncated protein could be created, in this instance this is the mechanism by which eukaryotic cells remove this protein from the cell
NonsenseNonsense variant is a single base change in the nucleotide sequence that causes the formation of a stop codon either forming a truncated protein or non-sense mediated decay of the transcript.
NonsynonymousNonsynonymous variant is a single base change in nucleotide sequence that changes the codon leading to the formation of an alternate amino acid.back to the top
OphthalmologyThe branch of medicine concerned with the study and treatment of disorders and diseases of the eye.back to the top
PhenotypeThe set of observable characteristics or traits of an individual.
PfamPfam is a database of protein domain families.
PseudonymousDataPseudonymous Data is a type of data that allows the potential, under certain circumstances, for the manager of the database to re-identify each individual at a future time, usually via a ‘key’ that decodes the pseudonym back into the NHS number. In this sense, pseudonymous data are neither identifiable nor anonymous because all personal identifiers have been removed but identification is still possible through the pseudonym.back to the top
RGSReference Genome Sequence (RGS) is a digital sequence assembled from sequencing the DNA from a number of donors.
ReadA Read is a fragment of data from the genome.back to the top
SenseSense variant is a single base change in nucleotide sequence that encodes the same amino acid, as several codons encode for the same amino acid.
SNPSingle Nucleotide Polymorphism (SNP) is a position in the genome where alternate bases are commonly found amongst a population.
SNVSingle Nucleotide Variant (SNV) is a position in an individual’s genome where an alternate base is found in the test genome relative to the reference genome.
SourceforgeThe Sourceforge website offers a repository for the source code, and tools that allow for it to be modified and updated in a way in which the whole community can contribute, but which can still be controlled by the original developers to ensure code quality.
SynonymousSynonymous variant is a single base change in nucleotide sequence that encodes the same amino acid, as several codons encode for the same amino acid.
SpliceSiteSplice-site is the position of two base pairs at the intron/exon boundary by which the process of splicing occurs to produce the mature mRNA transcript from the pre-mRNA.back to the top
VOUSVariant of Unknown Significance (VOUS) is a variation in a genetic sequence whose association with disease risk is unknown.back to the top
WESWhole Exome Sequencing (WES) is sequencing of exons only within a genome by NGS.
WGSWhole Genome Sequencing (WGS) is sequencing of the entire genome by NGS.back to the top
XlinkedX-linked describes the inheritance pattern of a genetic condition that is inherited on the X chromosome, hence males will definitely inherit the disorder as they only have one X chromosome whereas females may show milder symptoms of the condition depending on which genetic disorder it is.
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Clinical Bioinformatics: Unlocking Genomics in Healthcare
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