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Table 3 Samples in the unseen population dataset with discordant call between the genotypic algorithms

From: Quantitative prediction of integrase inhibitor resistance from genotype through consensus linear regression modeling

 

Genotypic algorithms

Linear models

 

ANRS (May 2011)

Rega v8.0.2

Stanford 6.0.11

First order

Second order

Samplea

mutations

call

mutations

call

mutations

call

mutations

BCO call

mutations

BCO call

L74ILM

72I, 74M

S

74M, 156N

I

74M

S

74M

S

74M

S

L74M, A91 T, T97A/T, F121Y

72I, 74M, 97A, 121Y

R

74M, 97A, 206S

I

74M, 97A, 121Y

I

74M, 91T, 97A, 119R, 121Y

R

74M, 91 T, 97A, 119R, 121Y

R

L74M, K103R, I135V, I200L

72I, 74M

S

74M

I

74M

S

74M, 135V, 200L

R

74M, 103R

R

L74M, V151A/V

72I, 74M

S

74M

I

74M, 151A

S

74M, 135V, 200L

R

74M, 103R

S

A91 T, F121Y

72I, 121Y

R

206S

S

121Y

I

91 T, 119R, 121Y

R

91T, 119R, 121Y

R

T97A

72I, 97A

S

97A, 206S

I

97A

S

25E, 97A

R

25E, 97A

S

E138E/K

72I

S

138K, 206S

S

138K

I

135V

S

-

S

E138E/K

-

S

138K

S

138K

I

25E

S

25E

S

E157Q

72I, 157Q

R

156N

S

157Q

S

-

S

-

S

E157Q

72I, 157Q

R

206S

S

157Q

S

135V

S

-

S

E157Q

157Q

R

-

S

157Q

S

-

S

-

S

E157Q

157Q

R

156 N, 206S

S

157Q

S

-

S

-

S

  1. aHXB2 reference amino acid is shown.
  2. The mutations on which the RAL S(usceptible)/I(ntermediate)/R(esistant) call is based, are listed. For the linear models, the call is R(esistant) if FC prediction is above the RAL biological cutoff (BCO = 2.0).