Stutter (MPS)
Definition
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 within the repeat from sequencing error). Both must be modelled by forensic-specific tools before allele calls are reported.
- Platform
- Massively parallel sequencing
- Length-based cause
- PCR slippage, as in CE stutter
- Sequence-based cause
- Single-nucleotide sequencing error
- Requires
- Forensic-specific allele-calling tools
Common questions
How does MPS stutter differ from stutter in capillary electrophoresis?+
CE only measures fragment length, so it sees one type of stutter, the n-1 slippage artefact. MPS reads the actual base sequence, which exposes a second category, sequence-based errors within the repeat region, that CE cannot detect at all.
Why can't generic sequencing software call MPS alleles correctly?+
General-purpose variant callers are built for the kind of variation found across a whole genome, not for the specific slippage and stutter patterns typical of short tandem repeats, so forensic MPS analysis relies on software purpose-built to model those artefacts.
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...
- Isoallele
- Two STR alleles that share the same repeat count (and therefore appear as the same allele on CE) but differ by a...
- 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...
- VCF
- Variant Call Format, the standard output from variant callers (GATK, FreeBayes). Records each variant position with reference allele, alternative allele(s), genotype likelihoods,...