NIPT Report

The NIPT Report for the VeriSeq NIPT Assay Software v2 – RUO contains the chromosome classification results formatted as one sample per row for each sample in the pool.

Column

Description

Preset Value Options

Type

Regex

batch_name

Batch name.

Not applicable.

text

^[a-zA-Z0-9_-]{1,36}$

sample_barcode

Unique sample barcode.

Not applicable.

text

^[a-zA-Z0-9_-]{1,36}$

sample_type

Sample type information provided from point of collection or lab user. Determines aneuploidy classification, aneuploidy reporting, and QC criteria.

One of the following:

• Singleton–Single embryo pregnancy.
• Twin–Multiple embryo pregnancy.
• Control–Control sample of known sex and aneuploidy classification.
• NTC–No template control sample (no DNA).
• Not Specified–A sample type was not provided for this sample.

enum

Values specified in Preset Value Options.

sex_chrom

Sex chromosome analysis requested. Determines the presentation of aneuploidy classification and sex chromosome information.

One of the following:

• Yes–Sex chromosome aneuploidy and sex reporting requested.
• No–Neither sex chromosome aneuploidy nor sex reporting requested.
• SCA–Sex chromosome aneuploidy reporting requested, sex reporting not requested.
• Not Specified–A sex chromosome reporting option was not provided for this sample.

The NIPT Report displays the values of yes, no, and sca as all lowercase.

enum

Values specified in Preset Value Options.

screen_type

Screening type.

One of the following:

• Basic- Screen chromosomes 13, 18, or 21.
• Genomewide- Screen entire genome.
• Not Specified–A screen type was not provided for this sample.

The NIPT Report displays the values of basic and genomewide as all lowercase.

 text

Values specified in Preset Value Options.

flowcell

Sequencing flow cell barcode.

Not applicable.

text

^[a-zA-Z0-9_-]{1,36}$

class_sx

Sex chromosome aneuploidy classification.

One of the following depending on sample type and sex chromosome reporting option selected:

• ANOMALY DETECTED—View the anomaly_description for anomaly specifics.
• NO ANOMALY DETECTED—Negative sample and sex not reported.
• NO ANOMALY DETECTED – XX—Negative sample with a female fetus.
• NO ANOMALY DETECTED – XY—Negative sample with male fetus.
• NOT REPORTABLE—Software could not report sex chromosome.
• NO CHR Y PRESENT—Twin pregnancy with no Y chromosome detected.
• CHR Y PRESENT—Twin pregnancy with Y chromosome detected.
• CANCELLED—Sample canceled by the user.
• INVALIDATED—Sample has failed QC or invalidated by the user.
• NOT TESTED—Sex chromosome was not tested.
• Not applicable— Category is not applicable to sample.

class_sx

Values specified in Preset Value Options.

class_auto

Classification for aneuploidies in autosomes. Reported as ANOMALY DETECTED if an anomaly within the selected screen type was detected for the sample.

One of the following:

• ANOMALY DETECTED—Autosomal chromosomal anomaly detected.
• NO ANOMALY DETECTED—No autosomal anomaly detected.
• CANCELLED—Sample cancelled by the user.
• INVALIDATED—Sample has failed QC or invalidated by the user.
• Not applicable— Category is not applicable to sample.

text

Values specified in Preset Value Options.

anomaly_description

ISCN-style string that describes all reportable anomalies. Multiple anomalies are separated by semicolons.

DETECTED:, followed by semicolon-separated strings concatenating the following formats, in chromosome order:

(\+|-)[12]?[0–9]

(del|dup)\([12]?[0–9]\)\(((p|q)[0–9]{1,2}(\.[0–9]{1,2})?){2}\)

XO|XXX|XXY|XYY

 

or NO ANOMALY DETECTED | not applicable | INVALIDATED | CANCELLED.

text

Semicolon-separated strings and other values described in the Anomaly Description Rules section.

qc_flag

QC analysis results.

Only the qc_flag value of PASS reports results. All other values do not.

One of the following:

• PASS
• FAIL
• CANCELLED
• INVALIDATED
• NTC_PASS

enum

Values specified in Preset Value Options.

qc_reason

QC failure information.

One of the following:

• NONE (QC status = PASS)
• FAILED iFACT
• DATA OUTSIDE OF EXPECTED RANGE
• FRAGMENT SIZE DISTRIBUTION OUTSIDE OF EXPECTED RANGE
• FLOWCELL DATA OUTSIDE OF EXPECTED RANGE
• FAILED TO ESTIMATE FETAL FRACTION
• SEQUENCING DATA OUTSIDE OF EXPECTED RANGE
• UNEXPECTED DATA
• NTC SAMPLE WITH HIGH COVERAGE
• CANCELLED
• INVALIDATED

text

Values specified in Preset Value Options.

ff

Estimated fetal fraction.

Percent sample cfDNA from fetus rounded to the nearest integer. Results less than 1% are presented as < 1%.

text

Not applicable.