Patents for immune repertoire sequencing protocols


#1

The patent application QUANTIFICATION OF ADAPTIVE IMMUNE CELL GENOMES IN A COMPLEX MIXTURE OF CELLS from Adaptive came to my email today.

Here’s the bulk of it:

A method for determining a ratio of T cells or B cells in a sample relative to the total number of input genomes contained in said sample comprising: A) amplifying by multiplex PCR and sequencing: i) rearranged CDR3 oligonucleotide sequences from T cell receptor (TCR) loci from T cells or Immunoglobulin (Ig) loci from B cells in said sample to obtain a total number of output biological sequences, each oligonucleotide sequence comprising a V segment and a J segment; ii) a first set of synthetic templates representing substantially all possible V segment and J segment combinations and each comprising one TCR or Ig V segment and one TCR or Ig J or C segment and a unique barcode which identifies said synthetic template as synthetic, and wherein each synthetic template comprises a unique combination of a V segment and J or C segment; B) determining an amplification factor for each synthetic template comprising a unique combination of a V segment and a J or C segment, wherein said amplification factor is represented by a total number of first synthetic templates observed from step A(ii) divided by a total input number of unique first synthetic templates input in step A(ii); C) determining the total number of T cells or B cells in the sample by dividing the total number of output biological sequences observed in step A(i) by the amplification factor from step B; D) amplifying by multiplex PCR and sequencing: i) one or more genomic control regions from DNA obtained from said sample to obtain a total number of output biological sequences for each genomic control region; and ii) a second set of synthetic templates comprising the sequence of one or more of said genomic control sequences, a unique barcode and a stretch of random nucleic acids, wherein each synthetic template is represented only once; E) determining an amplification factor for each of said genomic control region by dividing the total number of second synthetic templates amplified and sequenced in step D(ii) by the total input number of unique second synthetic templates amplified and sequenced in step D(ii); F) determining the total number of input genomes by dividing the total number of output biological sequences for each genomic control region from step D(i) by the corresponding amplification factor for that genomic control region from Step E; and G) determining the ratio of T cells or B cells contained in the sample relative to the number of total genomes in the sample by dividing the total number of T cells or B cells obtained in step C by the total number of input genomes obtained in step F.

Anyone know the status of other patent applications or issued patents for protocols?


#2

https://www.google.com/patents/US9234240


#3

Yes, this is S.Quake’s patent. I have one under review, it’s still at the stage of a patent application, It has not been granted.
George Gorgiou has one as well, possibly more:
https://www.google.com/patents/EP2572203A4?cl=en
There is this one as well and several more at the status of application: http://www.google.com/patents/WO2014144713A2?cl=en


#4

Robinson WH (Stanford) tried to patent “everything barcoded and/or single-cell” in US patent application 20150133317: IDENTIFICATION OF POLYNUCLEOTIDES ASSOCIATED WITH A SAMPLE. Currently only few of the 400+ initial claims are left and in my opinion even those were prior art when the application was filed. Best to my knowledge, Atreca had an exclusive license on this IP at some point, but I do not know whether this is still the case.