ADAPTIVE ORDER FULFILLMENT AND TRACKING METHODS AND SYSTEMS

1 . A genomic test processing system comprising:

an order management engine;

one or more order processing engines, comprising:

a receiving engine, to receive a state of an order from the order management engine;

an execution engine, to:

determine a sequence of steps to advance the received state of an order to a final state;

iteratively designate each step of the sequence of steps as completed before initiating the next step of the sequence of steps; and

advance the state of the order to a final state when a last step of the sequence of steps is completed; and

a broadcasting engine, to broadcast the final state of the order to the order management engine; and

wherein the order management engine causes one of the one or more order processing engines to generate a next-generation sequencing report from the final state of the order.

2 . The system of claim 1 , wherein the received state of an order indicates DNA processing of a specimen, the sequence of steps further comprising:

scraping a prepared FFPE slide to collect a sample of the specimen's tissue;

isolating DNA nucleotides from the sample;

amplifying the isolated nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

identifying genetic variants from the human reference genome in the sequenced nucleotides; and

generating a report from the identified genetic variants.

3 . The system of claim 1 , wherein the received state of an order indicates RNA processing of a specimen, the sequence of steps further comprising:

scraping a prepared FFPE slide to collect a sample of the specimen's tissue;

isolating RNA nucleotides from the sample;

amplifying the isolated nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

measuring an abundance of at least one of the mapped nucleotides; and

generating a report from the measured abundance of the at least one of the mapped nucleotides.

4 . The system of claim 1 , wherein a first order processing engine receives the state of an order indicating DNA processing of a specimen and a second order processing engine receives the state of the order indicating RNA processing of the specimen, further comprising:

at the first order processing engine:

scraping a prepared FFPE slide to collect a first sample of the specimen's tissue;

isolating DNA nucleotides from the first sample;

amplifying the isolated DNA nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

identifying genetic variants from the human reference genome in the sequenced nucleotides; and

generating a report from the identified genetic variants; and

at the second order processing engine:

scraping a prepared FFPE slide to collect a second sample of the specimen's tissue;

isolating RNA nucleotides from the second sample;

amplifying the isolated RNA nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

measuring an abundance of at least one of the mapped nucleotides; and

generating a report from the measured abundance of the at least one of the mapped nucleotides; and

wherein the first and the second order processing engines operate concurrently.

5 . The system of claim 2 , wherein:

one or more of the following steps occur at a first geographic location:

scraping a prepared FFPE slide to collect a sample of the specimen's tissue;

isolating DNA nucleotides from the sample;

amplifying the isolated nucleotides; and

sequencing the amplified nucleotides; and

one or more of the following steps occur in a cloud-based architecture:

mapping the sequenced nucleotide to a human reference genome;

identifying genetic variants from the human reference genome in the sequenced nucleotides; and

generating a report from the identified genetic variants.

6 . The system of claim 2 , wherein:

one or more of the following steps occur at a first geographic location:

scraping a prepared FFPE slide to collect a sample of the specimen's tissue;

isolating RNA nucleotides from the sample;

amplifying the isolated nucleotides; and

sequencing the amplified nucleotides; and

one or more of the following steps occur at a second geographic location:

mapping the sequenced nucleotides to a human reference genome;

measuring an abundance of at least one of the mapped nucleotides; and

generating a report from the measured abundance of the at least one of the mapped nucleotides.

7 . The system of claim 5 , wherein the report from the identified genetic variants also comprises information based on a database of information of individuals with a health condition similar to that of a patient who was a source of the specimen.

8 . The system of claim 6 , wherein the report from the measured abundance of the at least one of the mapped nucleotides also comprises information based on a database of information of individuals with a health condition similar to that of a patient who was a source of the specimen.

9 . The system of claim 1 , wherein the genomic test includes tumor-normal sequencing, and wherein a first order processing engine receives the state of an order indicating DNA processing of a normal specimen and a second order processing engine receives the state of the order indicating DNA processing of a tumor specimen, further comprising:

at the first order processing engine:

scraping a prepared FFPE slide to collect a sample of the normal specimen's tissue;

isolating normal DNA nucleotides from the normal sample;

amplifying the isolated normal nucleotides;

sequencing the amplified normal nucleotides;

mapping the sequenced normal nucleotides to a human reference genome; and

identifying genetic variants of the normal sample from the human reference genome in the sequenced nucleotides;

at the second order processing engine:

scraping a prepared FFPE slide to collect a sample of the tumor specimen's tissue;

isolating tumor DNA nucleotides from the tumor sample;

amplifying the isolated tumor nucleotides;

sequencing the amplified tumor nucleotides;

mapping the sequenced tumor nucleotides to a human reference genome;

identifying genetic variants of the tumor sample from the human reference genome in the sequenced nucleotides; and

generating a report from the identified genetic variants of the tumor sample based at least in part on the identified genetic variants of the normal sample.

10 . The system of claim 9 , wherein:

one or more of the following steps occur at a first geographic location:

scraping a prepared FFPE slide to collect a sample of the normal specimen's tissue;

isolating normal DNA nucleotides from the normal sample;

amplifying the isolated normal nucleotides;

sequencing the amplified normal nucleotides;

scraping a prepared FFPE slide to collect a sample of the tumor specimen's tissue;

isolating tumor DNA nucleotides from the tumor sample;

amplifying the isolated tumor nucleotides;

sequencing the amplified tumor nucleotides; and

one or more of the following steps occur in a cloud-based architecture:

mapping the sequenced tumor nucleotides to a human reference genome;

mapping the sequenced normal nucleotides to a human reference genome;

identifying genetic variants of the tumor sample from the human reference genome in the sequenced nucleotides;

identifying genetic variants of the normal sample from the human reference genome in the sequenced nucleotides; and

generating a report from the identified genetic variants of the tumor sample based at least in part on the identified genetic variants of the normal sample.

11 . The system of claim 1 , wherein the received state of an order indicates DNA processing of a liquid biopsy specimen, the sequence of steps further comprising:

removing cells from the liquid biopsy specimen to collect a cell-free sample of the specimen;

isolating DNA nucleotides from the cell-free sample;

amplifying the isolated nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

identifying genetic variants from the human reference genome in the sequenced nucleotides; and

generating a report from the identified genetic variants.

12 . The system of claim 1 , wherein the received state of an order indicates DNA processing of a specimen, the sequence of steps further comprising:

scraping a prepared FFPE slide to collect a sample of the specimen's tissue;

isolating DNA nucleotides from the sample;

amplifying the isolated nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

identifying genetic variants from the human reference genome in the sequenced nucleotides;

generating a tumor mutational burden (TMB) score;

generating a microsatellite instability (MSI) score; and

generating a report from the identified genetic variants, TMB score, and MSI score.

13 . The system of claim 1 , wherein the received state of an order indicates DNA processing of a blood specimen, the sequence of steps further comprising:

extracting peripheral whole blood to collect a sample of the specimen;

isolating DNA nucleotides from the sample;

amplifying the isolated nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

identifying genetic variants from the human reference genome in the sequenced nucleotides;

generating a microsatellite instability (MSI) score; and

generating a report from the identified genetic variants and MSI score.

14 . The system of claim 1 , wherein the received state of an order indicates DNA processing of a specimen, the sequence of steps further comprising:

scraping a prepared FFPE slide to collect a sample of the specimen's tissue;

isolating DNA nucleotides from the sample;

amplifying the isolated nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

identifying genetic variants from the human reference genome in the sequenced nucleotides;

identifying one or more copy number alterations; and

generating a report from the identified genetic variants and copy number alterations.

15 . The system of claim 1 , wherein the received state of an order indicates RNA processing of a specimen, the sequence of steps further comprising:

scraping a prepared FFPE slide to collect a sample of the specimen's tissue;

isolating RNA nucleotides from the sample;

amplifying the isolated nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

measuring an abundance of at least one of the mapped nucleotides; and

identifying one or more fusions; and

generating a report from the measured abundance of the at least one of the mapped nucleotides and identified fusions.

16 . A method for genomic test processing carried out using an order management engine and one or more order processing engines including a receiving engine and an execution engine, comprising:

at the receiving engine:

receiving a state of an order from the order management engine;

at the execution engine:

determining a sequence of steps to advance the received state of an order to a final state;

iteratively designating each step of the sequence of steps as completed before initiating the next step of the sequence of steps; and

advancing the state of the order to a final state when a last step of the sequence of steps is completed; and

at the broadcasting engine:

broadcasting the final state of the order to the order management engine, wherein the order management engine causes one of the one or more order processing engines to generate a next-generation sequencing report from the final state of the order.

17 . The method of claim 16 , wherein the received state of an order indicates DNA processing of a specimen, the method further comprising:

scraping a prepared FFPE slide to collect a sample of the specimen's tissue;

isolating DNA nucleotides from the sample;

amplifying the isolated nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

identifying genetic variants from the human reference genome in the sequenced nucleotides; and

generating a report from the identified genetic variants.

18 . The method of claim 16 , wherein the received state of an order indicates RNA processing of a specimen, the method further comprising:

scraping a prepared FFPE slide to collect a sample of the specimen's tissue;

isolating RNA nucleotides from the sample;

amplifying the isolated nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

measuring an abundance of at least one of the mapped nucleotides; and

generating a report from the measured abundance of the at least one of the mapped nucleotides.

19 . The method of claim 16 , further comprising:

receiving, by a first order processing engine, the state of an order indicating DNA processing of a specimen, comprising:

scraping a prepared FFPE slide to collect a first sample of the specimen's tissue;

isolating DNA nucleotides from the first sample;

amplifying the isolated DNA nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

identifying genetic variants from the human reference genome in the sequenced nucleotides; and

generating a report from the identified genetic variants; and

receiving, by a second order processing engine, the state of the order indicating RNA processing of the specimen, comprising:

scraping a prepared FFPE slide to collect a second sample of the specimen's tissue;

isolating RNA nucleotides from the second sample;

amplifying the isolated RNA nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

measuring an abundance of at least one of the mapped nucleotides; and

generating a report from the measured abundance of the at least one of the mapped nucleotides,

wherein the first and the second order processing engines operate concurrently.

20 . The method of claim 17 , wherein:

one or more of the following steps occur at a first geographic location:

scraping a prepared FFPE slide to collect a sample of the specimen's tissue;

isolating DNA nucleotides from the sample;

amplifying the isolated nucleotides; and

sequencing the amplified nucleotides; and

one or more of the following steps occur in a cloud-based architecture:

mapping the sequenced nucleotide to a human reference genome;

identifying genetic variants from the human reference genome in the sequenced nucleotides; and

generating a report from the identified genetic variants.

21 . The method of claim 17 , wherein:

one or more of the following steps occur at a first geographic location:

scraping a prepared FFPE slide to collect a sample of the specimen's tissue;

isolating RNA nucleotides from the sample;

amplifying the isolated nucleotides; and

sequencing the amplified nucleotides; and

one or more of the following steps occur at a second geographic location:

mapping the sequenced nucleotides to a human reference genome;

measuring an abundance of at least one of the mapped nucleotides; and

generating a report from the measured abundance of the at least one of the mapped nucleotides.

22 . The method of claim 20 , wherein the report from the identified genetic variants also comprises information based on a database of information of individuals with a health condition similar to that of a patient who was a source of the specimen.

23 . The method of claim 21 , wherein the report from the measured abundance of the at least one of the mapped nucleotides also comprises information based on a database of information of individuals with a health condition similar to that of a patient who was a source of the specimen.

24 . The method of claim 16 , wherein the genomic test includes tumor-normal sequencing, and wherein a first order processing engine receives the state of an order indicating DNA processing of a normal specimen and a second order processing engine receives the state of the order indicating DNA processing of a tumor specimen, further comprising:

at the first order processing engine:

scraping a prepared FFPE slide to collect a sample of the normal specimen's tissue;

isolating normal DNA nucleotides from the normal sample;

amplifying the isolated normal nucleotides;

sequencing the amplified normal nucleotides;

mapping the sequenced normal nucleotides to a human reference genome; and

identifying genetic variants of the normal sample from the human reference genome in the sequenced nucleotides;

at the second order processing engine:

scraping a prepared FFPE slide to collect a sample of the tumor specimen's tissue;

isolating tumor DNA nucleotides from the tumor sample;

amplifying the isolated tumor nucleotides;

sequencing the amplified tumor nucleotides;

mapping the sequenced tumor nucleotides to a human reference genome;

identifying genetic variants of the tumor sample from the human reference genome in the sequenced nucleotides; and

generating a report from the identified genetic variants of the tumor sample based at least in part on the identified genetic variants of the normal sample.

25 . The method of claim 24 , wherein:

one or more of the following steps occur at a first geographic location:

scraping a prepared FFPE slide to collect a sample of the normal specimen's tissue;

isolating normal DNA nucleotides from the normal sample;

amplifying the isolated normal nucleotides;

sequencing the amplified normal nucleotides;

scraping a prepared FFPE slide to collect a sample of the tumor specimen's tissue;

isolating tumor DNA nucleotides from the tumor sample;

amplifying the isolated tumor nucleotides;

sequencing the amplified tumor nucleotides; and

one or more of the following steps occur in a cloud-based architecture:

mapping the sequenced tumor nucleotides to a human reference genome;

mapping the sequenced normal nucleotides to a human reference genome;

identifying genetic variants of the tumor sample from the human reference genome in the sequenced nucleotides;

identifying genetic variants of the normal sample from the human reference genome in the sequenced nucleotides; and

generating a report from the identified genetic variants of the tumor sample based at least in part on the identified genetic variants of the normal sample.

26 . The method of claim 16 , wherein the received state of an order indicates DNA processing of a liquid biopsy specimen, the sequence of steps further comprising:

removing cells from the liquid biopsy specimen to collect a cell-free sample of the specimen;

isolating DNA nucleotides from the cell-free sample;

amplifying the isolated nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

identifying genetic variants from the human reference genome in the sequenced nucleotides; and

generating a report from the identified genetic variants.

27 . The method of claim 16 , wherein the received state of an order indicates DNA processing of a specimen, the sequence of steps further comprising:

scraping a prepared FFPE slide to collect a sample of the specimen's tissue;

isolating DNA nucleotides from the sample;

amplifying the isolated nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

identifying genetic variants from the human reference genome in the sequenced nucleotides;

generating a tumor mutational burden (TMB) score;

generating a microsatellite instability (MSI) score; and

generating a report from the identified genetic variants, TMB score, and MSI score.

28 . The method of claim 16 , wherein the received state of an order indicates DNA processing of a blood specimen, the sequence of steps further comprising:

extracting peripheral whole blood to collect a sample of the specimen;

isolating DNA nucleotides from the sample;

amplifying the isolated nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

identifying genetic variants from the human reference genome in the sequenced nucleotides;

generating a microsatellite instability (MSI) score; and

generating a report from the identified genetic variants and MSI score.

29 . The method of claim 16 , wherein the received state of an order indicates DNA processing of a specimen, the sequence of steps further comprising:

scraping a prepared FFPE slide to collect a sample of the specimen's tissue;

isolating DNA nucleotides from the sample;

amplifying the isolated nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

identifying genetic variants from the human reference genome in the sequenced nucleotides;

identifying one or more copy number alterations; and

generating a report from the identified genetic variants and copy number alterations.

30 . The method of claim 16 , wherein the received state of an order indicates RNA processing of a specimen, the sequence of steps further comprising:

scraping a prepared FFPE slide to collect a sample of the specimen's tissue;

isolating RNA nucleotides from the sample;

amplifying the isolated nucleotides;

sequencing the amplified nucleotides;

mapping the sequenced nucleotides to a human reference genome;

measuring an abundance of at least one of the mapped nucleotides; and identifying one or more fusions; and

generating a report from the measured abundance of the at least one of the mapped nucleotides and identified fusions.