Isoallele
Definition
Two STR alleles that share the same repeat count (and therefore appear as the same allele on CE) but differ by a single nucleotide within the repeat sequence. MPS resolves isoalleles; CE does not. Resolution of isoalleles increases the discrimination power of the DNA profile.
- Detected by
- Massively parallel sequencing (MPS)
- Missed by
- Capillary electrophoresis (CE)
- Cause
- Single nucleotide variant within the repeat
- Effect on CE profile
- Appears as an ordinary allele, no extra peak
Common questions
Why does isoallele resolution matter for a DNA case?+
Two individuals with genuinely different sequences at a locus can look identical on a CE electropherogram if their alleles happen to be isoalleles. MPS separates them, which can turn an apparent shared allele into two distinguishable ones and improve discrimination between similar profiles.
Does an isoallele change the reported repeat number?+
No. The repeat count used for the CE-style allele call stays the same; only the underlying nucleotide sequence differs. MPS reports this as a sequence-based allele variant rather than a new numeric allele.
Related terms
- BAM File
- Binary Alignment/Map format, the compressed binary version of a SAM file. Stores aligned reads with their mapping positions, quality scores, and alignment...
- FASTQ
- The standard sequencing output file format containing four-line records per read: identifier, nucleotide sequence, separator, and Phred quality score string. All MPS...
- Phred Quality Score (Q)
- A logarithmic probability score for base-call accuracy. Q30 = 99.9% accuracy (1 in 1000 error probability). Q20 = 99% accuracy. Most forensic...
- Stutter (MPS)
- In MPS, stutter includes both length-based stutter (as in CE, an n-1 repeat artefact from PCR slippage) and sequence-based stutter (single-nucleotide errors...
- VCF
- Variant Call Format, the standard output from variant callers (GATK, FreeBayes). Records each variant position with reference allele, alternative allele(s), genotype likelihoods,...