Methods, systems and non-transitory machine-readable storage medium are provided to mitigate insertion errors and deletion errors in STR sequences and improve accuracy in determination of the number of repeats. A method includes determining one or more optimum clusters for a set of flow space signal measurements, wherein at least one of the optimum clusters is associated with a homopolymer length, modifying a base call at the position in the repeat region sequence to the homopolymer length associated with the optimum cluster to produce a corrected repeat region sequence, thereby correcting an insertion error or a deletion error. The method may further include detecting variations in the flanks associating those variations with the length of the STR.

Methods, systems and non-transitory machine-readable storage medium are provided to mitigate insertion errors and deletion errors in STR sequences and improve accuracy in determination of the number of repeats. A method includes determining one or more optimum clusters for a set of flow space signal measurements, wherein at least one of the optimum clusters is associated with a homopolymer length, modifying a base call at the position in the repeat region sequence to the homopolymer length associated with the optimum cluster to produce a corrected repeat region sequence, thereby correcting an insertion error or a deletion error. The method may further include detecting variations in the flanks associating those variations with the length of the STR.

A DNA analysis method and a DNA analyzing device using terahertz wave capable of accurately determining a type of cancer from DNA using terahertz wave are disclosed. The DNA analysis method according to the present invention comprises: (a) irradiating terahertz wave onto methylated DNA; (b) detecting the terahertz wave reflected from the methylated DNA; (c) detecting a peak of a waveform of the terahertz wave detected in the step (b); and (d) determining type of cancer from the peak detected in the step (c).

A DNA analysis method and a DNA analyzing device using terahertz wave capable of accurately determining a type of cancer from DNA using terahertz wave are disclosed. The DNA analysis method according to the present invention comprises: (a) irradiating terahertz wave onto methylated DNA; (b) detecting the terahertz wave reflected from the methylated DNA; (c) detecting a peak of a waveform of the terahertz wave detected in the step (b); and (d) determining type of cancer from the peak detected in the step (c).

The present invention is focused on a method, kit and system for determining the presence or absence of minimal residual disease in a subject who has been treated for a proliferative disease wherein said method, kit and system comprise: (A) amplifying and sequencing at least one nucleotide sequence comprised in genomic DNA from a biological sample obtained from said subject prior to treatment for said disease, to obtain a first list of characters reading from left to right; (B) amplifying and sequencing at least one nucleotide sequence comprised in genomic DNA from a biological sample obtained from said subject after treatment for said disease, to obtain a second list of characters reading from left to right,
wherein when a nucleotide sequence is mutated it is a genetic marker for said proliferative disease; (C) determining, for each second list of characters obtained in step (B), the degree of similarity, DS, with each first list of characters obtained in step (A); (D) selecting, for each second list of characters obtained in step (B), the DS of highest value, DS.sub.HV; (E) adding up the number of second lists of characters which have a DS.sub.HV that is greater than a threshold value, T, to obtain L.sub.c, (F) adding up the total number of second lists of characters, L.sub.t; (G) calculating the level of minimal residual disease, MRD, according to any of the following formulae:

MRD=(L.sub.c×k)/(L.sub.t×D)

or

MRD=L.sub.c/L.sub.t

or

MRD=g×L.sub.c×(D/k)/L.sub.t.sup.2; (H) determining (i) the minimum variant read frequency, min VRF, of said genetic marker, (ii) the limit of detection, D-limit, of said genetic marker (iii) the average mutation noise, avMut and (iv) the average position noise, avPos; (I) determining the experimental sensitivity, ES, from the greater of the min VRF, D-limit, avMut and avPos or from the greater of min VRF and D-limit; (J) determining the presence or absence of minimal residual disease in said subject

The present invention is focused on a method, kit and system for determining the presence or absence of minimal residual disease in a subject who has been treated for a proliferative disease wherein said method, kit and system comprise: (A) amplifying and sequencing at least one nucleotide sequence comprised in genomic DNA from a biological sample obtained from said subject prior to treatment for said disease, to obtain a first list of characters reading from left to right; (B) amplifying and sequencing at least one nucleotide sequence comprised in genomic DNA from a biological sample obtained from said subject after treatment for said disease, to obtain a second list of characters reading from left to right,
wherein when a nucleotide sequence is mutated it is a genetic marker for said proliferative disease; (C) determining, for each second list of characters obtained in step (B), the degree of similarity, DS, with each first list of characters obtained in step (A); (D) selecting, for each second list of characters obtained in step (B), the DS of highest value, DS.sub.HV; (E) adding up the number of second lists of characters which have a DS.sub.HV that is greater than a threshold value, T, to obtain L.sub.c, (F) adding up the total number of second lists of characters, L.sub.t; (G) calculating the level of minimal residual disease, MRD, according to any of the following formulae:

MRD=(L.sub.c×k)/(L.sub.t×D)

or

MRD=L.sub.c/L.sub.t

or

MRD=g×L.sub.c×(D/k)/L.sub.t.sup.2; (H) determining (i) the minimum variant read frequency, min VRF, of said genetic marker, (ii) the limit of detection, D-limit, of said genetic marker (iii) the average mutation noise, avMut and (iv) the average position noise, avPos; (I) determining the experimental sensitivity, ES, from the greater of the min VRF, D-limit, avMut and avPos or from the greater of min VRF and D-limit; (J) determining the presence or absence of minimal residual disease in said subject

Provided herein are compositions, devices, systems and methods for the generation and use of biomolecule-based information for storage. Further described herein are highly efficient methods for long term data storage with 100% accuracy in the retention of information. Additionally, devices described herein for de novo synthesis of oligonucleic acids encoding information related to the original source information may have a flexible material for oligonucleic acids extension.

Provided herein are compositions, devices, systems and methods for the generation and use of biomolecule-based information for storage. Further described herein are highly efficient methods for long term data storage with 100% accuracy in the retention of information. Additionally, devices described herein for de novo synthesis of oligonucleic acids encoding information related to the original source information may have a flexible material for oligonucleic acids extension.

The invention provides various orthogonal nucleotide analogues and methods for using combinations of said various orthogonal nucleotide analogues for sequencing by synthesis.

The invention provides various orthogonal nucleotide analogues and methods for using combinations of said various orthogonal nucleotide analogues for sequencing by synthesis.