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Incomplete lineage sorting should be apparent as "shared derived mutations" (defined as derived mutations that occur in both lineages).
Mutator mutations, defined as genetic changes which increase the rate of genetic change, including both single base changes and chromosomal instability, may accelerate this process.
Mitochondrial mutations, defined as sequence differences between tumors and germ line DNA were identified in 17/22 (77%) samples tested.
Hence, to enhance the sensitivity of our analysis we focused on mutations that reflect the most recent rounds of replication, "private site mutations", defined as a mutation found in only one of the (N = 105) viral genomes sequenced.
To accomplish this, we excluded exceedingly rare drug-resistance mutations defined as those mutations present at a frequency below 0.5% among treated individuals in the subtype having the highest prevalence of that mutation.
All other mutations defined as non-disruptive mutations affect p53 function in a limited fashion.
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However, when considering the most clinically relevant types of mutation defined as functional mutations (exonic: missense, stop, frameshift, and in-frame indel mutations and splicing variants) >99% of genes were not more mutated in FFPE than FF data sets (Supplementary Figure S20B).
Regardless of the absence of a familial history of hereditary cancer, a germline mutation in p53 was identified (a missense mutation defined as c.722 C>T, p.Ser241Phe).
The patient is hemizygous in the GLA gene (located on the X chromosome) for a mutation defined as c.1277-1278delAA, whish is predicted to result in frameshift and premature protein termination p.Lys426ArgfsStop24.
Among common mutations (defined herein as mutations observed in multiple individuals) private alleles predominated.
The altered thermo-sensitivity of these mutations, defined here as slope, is very subtle, yet is still significant (see Additional file 12: Table S3).
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