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Sanger sequence:

A method to determine the order of DNA bases by chain-terminating dideoxynucleotides by DNA polymerase. Sanger sequencing is the current gold standard for validating single nucleotide variants identified through massively parallel sequencing. Typically used for DNA sequence fragments ~500 nucleotides in length.

Segregation analysis (Segregation):

To compare the phenotypes of individuals in families to genotypes to determine the most likely mode of inheritance of a particular disease, or if a genetic variant is inherited by all individual in a family with a particular disease. Can also refer to disjunction of homologous chromosomes at meiosis.

Sequencing:

To determine the order nucleotides in a segment of DNA or RNA, which define the amino acids in a protein. Can also refer to a pattern of dysmorphic features caused by different etiologies.

Sequence Capture:

The massively parallel replacement for PCR. The process of simultaneously isolating thousands or millions of regions of the genome prior to massively parallel sequencing. also known as targeted sequence capture or targeted genomic enrichment.

Sex chromosome:

The chromosomes which determine gender in an organism. In humans the sex chromosomes are the 23rd pair of chromosomes, X and Y. Females have two X chromosomes and males have an X and Y chromosome.

Sex-linked trait:

A trait due to a gene alteration on the X or Y chromosome.

Simplex family:

A family in which only one family member is affected by a disease or disorder.

Single gene disorder:

A genetic disorder caused by alterations in a single gene, such as Sickle cell disease, Duchenne muscular dystrophy. Compare to polygenic, complex, or multifactorial disorder.

Single Nucleotide Polymorphism (SNP):

The alteration of a single nucleotide or base pair of DNA in the human genome. This type of variation is common and can be characterized in populations. (also known as polymorphism)

SNP:

See single nucleotide polymorphism

SNV:

Single nucleotide variant

Sporadic case:

The occurrence of a genetic disorder in one individual of a family due to a new mutation or by chance. These disorders have a low likelihood of recurring in the family. (also known as isolated case)

Splice-site variant (splicing variant):

A nucleotide change which alters or removes the specific sequence necessary for excising out of an intron. Variants which alter this sequence can result in the retention of an intron of the loss of an exon in the mature messenger RNA, thereby resulting in an altered protein product. (may be denoted splice-3 if in the 3’ end of a splice site, or splice-5 if at the 5’ end of a splice site)

Stop codon:

One of three amino acid sequences (codons) which result in the termination of a polypeptide. The three stop codons in humans are UAG, UAA, and UGA. (also known as Termination codon)

Stop-gain variant:

A DNA sequence change which results in a new stop codon.

Stop-lost variant:

A DNA sequence change which results in a loss of a stop codon.

STS:

Sequence tagged site

syn:

See synonymous

Synonymous variant:

A nucleotide change in the DNA which does not alter the protein sequence. (also known as silent allele; coding-synonymous).