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They then looked for variants present only in affected people, and came up with one candidate gene.
‡Resequencing referenced the M. leprae TN standard genomic sequence, identified 13 variants present only in 3I-2-v1 (2 SNP, 2 insertion/deletions) or 3I-2-v15 3I-2-v15 3I-2-v15erentiated the strains.
As might be expected, the global post-vaccination data set shows more sequence variability than the Danish pre-/early-vaccination era data set, whereas the latter shows relatively more singletons, i.e. variants present only in a single sequence.
A total of 337 novel, deleterious variants present only in the affected members of Families I, II, and III were identified at an average of 112 variants per family (Table 2, Additional files 1: Table S1A, B, C); 689 novel, deleterious variants were identified in the 22 probands at an average of 30 variants per proband (Table 2, Additional files 2: Table S2A, B).
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Typically, these frequency cut-off values are set at >70%%, implying that only variants fixed within a population are identified i.e. variants present at only >70%% of the sequencing reads are analysed [ 6, 8].
When more than one splice variant, or size variant was present, only the longest protein sequence was kept for analysis.
In each experiment, the authors used mRNA from just 50 neurons from the brains of people with or without sporadic Alzheimer's, because averaging across large neuronal populations could mask variants present in only a few cells.
Concerning the acquired variants (present in only one out of the four lines) we identified 39 SNPs in the U regions.
We term variants present in only one individual i.e. with frequency of 0.1%, 'rare', those with frequency between 0.2 5% (i.e. present in 2 50 individuals) 'low-frequency' and those with frequency >5% (i.e. present in >50 individuals) 'common'common
Class B variants are present only in eudicots.
Ideally the causal variant is present only in affected individuals, but the possibility of unaffected carriers has to be taken into account because of incomplete penetrance, or later debut of the disease.
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