storage and management of samples will be in line with the Rules for
Handling Pathological Tissue Samples for Genome Research stipulated
by the Japanese Society of Pathology. Standard operating procedures
will be drawn up during FY2022 to ensure that storage and management
are carried out according to standardized methods that comply with
international norms.
Strict compliance with the standard operating procedures is also
obligatory when outsourcing to a sequencing company or storage in a
cooperating medical institution is desired.
3) Sequencing
Samples submitted by medical institutions will be sequenced by
sequencing companies. To ensure standardization of sequencing methods
in compliance with international norms, sequencing companies will have to
draw up standard operating procedures and submit an outline to the
Analysis and Data Center during FY2022.
o Quality control
Sequencing companies will evaluate the quality and quantity of the data
before human genome mapping on the basis of the criteria established
by the Expert Committee to obtain data that meet the reference values.
Sequencing companies will be under the obligation to cooperate with
external accuracy management carried out by the MHLW Science
Research Group for promotion of whole genome analysis of cancer and
establishment of a system for technology assessment related to whole
genome analysis of each individual patient and its clinical application, a
center for data analysis and storage, information security and patient
confidentiality, and Ethical Legal and Social Implications (ELSI)
(tentative name), using the sequencing accuracy values, the relevant
summary values, and the pre-mapping quality control values of
sequencing companies.

4) Clinical genome analysis and report preparation at medical institutions or
the Analysis and Data Center
The Analysis and Data Center will carry out clinical genome analysis of
FASTQ data sent by outsourced sequencing companies, and prepare
reports. With new mutations, advanced cross-sectional analysis will be
performed using the FASTQ data, etc. to determine their medical
significance.
The systems needed for this are as follows.
o Information management
Centralized management system
The Analysis and Data Center will establish a centralized management
system for centralized management and utilization of whole genome
data, clinical information, samples, and information on samples. The
centralized management system will be capable of managing the status
of patients’ informed consent, information on samples, information on
data transfer, quality control (QC) results, the progress of genome

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