Table 1 Variant genotypes compared for concordance between the array-based and sequence based methods to determine concordance, sensitivity and discrepancy between the two assays (a) and measures of concordance (b)

a) NGS-based genotypes

Array-based genotypes (gold standard)

Homozygous reference

Heterozygous

Homozygous alternative

AA

AB

BB

Homozygous reference

AA

a

b

c

Heterozygous

AB

d

e

f

Homozygous alternative

BB

g

h

i

Genotype not identified

–

k

l

m

b)

Measures of concordance

SNP concordance

$\frac{\left(a+b+c+d+e+f+g+h+i\right)}{\left(a+b+c+d+e+f+g+h+i+k+l+m\right)}$

Genotype concordance

$\frac{\left(a+e+i\right)}{\left(a+b+c+d+e+f+g+h+i\right)}$

Non-reference sensitivity

$\frac{\left(e+f+h+i\right)}{\left(b+c+e+f+h+i+l+m\right)}$

Non-reference discrepancy

$\frac{\left(b+c+d+f+g+h\right)}{\left(b+c+d+e+f+g+h+i\right)}$