Molecular, Genetics & Specimen Calculations
Every molecular, genetics & specimen calculations calculator on CalcEngines — unit converters, derived indices and interpretive tools, each with its formula, a worked example and the reference intervals it is judged against.
24 calculators in this section
- ACMG Variant Classification InterpreterTurn counts of ACMG/AMP criteria into Pathogenic, Likely pathogenic, Uncertain significance, Likely benign or Benign. The headline is the Tavtigian point score that ClinGen expert panels now use; the 2015 Table 5 verdict is printed beside every result, because that is what the report in front of you was written against.
- Cell-Free DNA Fetal Fraction CalculatorThe placental share of the cell-free DNA in a maternal plasma sample — the quality metric that decides whether a prenatal screening result can be issued at all, and why a no-call is not a negative result.
- Copy Number from Log2 Ratio CalculatorCopy number as 2 × 2^log2 ratio for an autosomal locus — and the purity correction that has to be applied before that reading means anything in a tumour sample.
- CYP2D6 Activity Score InterpreterAdd the two allele activity values and read the sum against the current CPIC boundaries — which moved in the 2019–2020 CPIC/DPWG consensus, taking an activity score of 1 out of normal and into intermediate. The score belongs to the gene, not to the drug, and the page asks which drug you mean because the consequence inverts.
- DNA Copy Number CalculatorConvert a mass of double-stranded DNA into a number of molecules, using 660 g/mol per base pair and Avogadro's number — the calculation behind every qPCR standard curve made from a plasmid or an amplicon.
- DNA Molarity (nM) CalculatorConvert a double-stranded DNA concentration in ng/µL into nanomolar, using 660 g/mol per base pair — the calculation that normalises sequencing libraries, where molarity and not mass is what gets loaded.
- Donor Chimerism Percentage CalculatorPercentage donor from the peak areas of one informative STR marker after transplantation — and why the direction of travel across serial samples carries more information than any single figure.
- Hardy-Weinberg Carrier Frequency CalculatorFrom the prevalence of an autosomal recessive condition to the proportion of the population who carry one copy — with the assumptions Hardy-Weinberg needs, and the two situations in which they fail exactly when you need them.
- Microsatellite Instability (MSI) InterpreterRead an MSI-PCR result and a mismatch repair immunohistochemistry panel together — the five Bethesda loci, the two obligate heterodimers, the reflex testing MLH1 loss demands, and what to do when the two methods disagree.
- Mitochondrial Heteroplasmy InterpreterA heteroplasmy percentage means almost nothing without the variant it belongs to and the tissue it was measured in. Blood under-represents the burden for several common variants and falls with age; the threshold effect differs from one variant to the next; and for some variants no validated threshold exists at all, which this page says rather than supplying one.
- NGS Coverage Depth CalculatorMean coverage from reads, read length and target size by the Lander-Waterman relation — and why the mean is the wrong number to report, because coverage is never evenly distributed across a target.
- NGS Run Quality InterpreterWhether a sequencing run or a sample within it is fit to report, from Q30 against the instrument's own read-length-specific specification, the coverage distribution across the target, the duplication rate and the on-target fraction. No professional body publishes universal pass marks, and this page does not invent any.
- NGS Variant Confirmation InterpreterWhether a next-generation sequencing call needs orthogonal confirmation before it is reported, from its depth, allele fraction, strand support, genomic context and what it is being reported as. The two published threshold sets disagree with each other, and the page shows you where you are against both.
- NIPT Positive Predictive Value CalculatorA cell-free DNA screen came back high risk. This works out the probability that the fetus is actually affected, from the published detection rate and false positive rate for that specific condition and the prior risk you supply — and shows how steeply that probability falls as the condition gets rarer.
- Nucleic Acid Concentration from A260 CalculatorTurn an A260 reading into a DNA or RNA concentration with the appropriate extinction factor, and read the A260/A280 ratio alongside it — absorbance tells you how much is there, not whether it is intact.
- Oligonucleotide Resuspension CalculatorHow much buffer a lyophilised oligo needs to reach a target stock concentration — and why the OD₂₆₀ figure on the tube converts to micrograms and nanomoles differently for every oligo you order.
- PCR Fold Amplification CalculatorTheoretical yield as (1 + E) raised to the number of cycles — and what the exponent does to a small efficiency deficit, which is why qPCR efficiency is measured rather than assumed.
- PCR Master Mix CalculatorWork out how much of one component a batch of PCR reactions needs, with the overage that stops the last tube coming up short — and see why the same overage has to be applied to every component alike.
- PCR Primer Melting Temperature (Tm) CalculatorEstimate a primer's Tm by the Wallace rule or the GC/salt-adjusted formula from its base composition — two rules of thumb that are useful for a sanity check and are not what a design tool uses.
- qPCR Efficiency Calculator from Standard CurveTurn the slope of a Ct-against-log-quantity standard curve into an amplification efficiency, and read it against the 90–110% window that decides whether the 2⁻ΔΔCt method is safe to use at all.
- qPCR ΔΔCt Fold Change CalculatorRelative expression by the Livak method: two ΔCt values, one ΔΔCt, and 2 raised to its negative. The arithmetic is trivial; the assumption underneath it is that both assays amplify at 100% efficiency.
- Residual Carrier Risk CalculatorThe Bayesian posterior after a negative carrier screen, from the prior carrier frequency and the panel's detection rate — because a negative screen lowers the risk and never removes it.
- Tumour Mutational Burden (TMB) CalculatorCountable mutations divided by the megabases of coding sequence the assay actually interrogated — and the reason a TMB of 10 on one panel is not a TMB of 10 on another.
- Variant Allele Frequency (VAF) CalculatorVariant reads as a percentage of total reads at a position — and what a VAF away from 50% or 100% is telling you, from mosaicism and copy-number change to clonal haematopoiesis in a blood sample used as a germline reference.