Reproductive genetics, modelled to the chromosome and the allele

The genetic work-up is where the decision starts

Before any embryo is biopsied, someone has to decide that genetics is indicated. The genetic work-up record is the geneticist's one-page view of a patient file: the karyotype formula and its narrative interpretation alongside the reproductive carrier screens that change management most often, CFTR, Fragile-X and spinal muscular atrophy, closing with a consolidated overall assessment. The indication is chosen from a seeded list rather than typed, so the reason genetics was involved stays reportable across the cohort. Once the assessment is final the record can be locked against further editing.

• Built screen set: list, create form and detail view with inline edit
• Indication drawn from eight seeded genetic indications
• Karyotype formula and interpretation held as separate fields
• Lock flag freezes the finalised assessment

One header per test, every matrix hanging off it

The PGT result header is the parent record for any preimplantation genetic test ordered on a treatment cycle. It names the test category, the embryo and the biopsy material, the indication from a seeded nine-item list, the referral laboratory, the dispatch and result dates, the top-line outcome and the embryo's disposition afterwards. That last field matters more than it looks: recording whether a tested embryo was transferred, frozen or discarded is what lets a centre audit its own PGT practice rather than only its PGT results. Every detailed result matrix described below attaches to this header, so a verdict can always be traced back to the run that produced it.

• Built screen set, grouped as Patient and Cycle, Investigation, Result
• Biopsy material recorded as blastomere, trophectoderm or polar body
• Sent date and result date held separately, giving turnaround time
• Embryo disposition after result: transferred, frozen or discarded

Array CGH results held chromosome by chromosome

This is the part that distinguishes the system. An array-CGH or NGS comprehensive-chromosome-screening run is modelled as three linked levels rather than one summary line. The parent level carries the platform, the embryo-level ploidy call, the affected chromosomes, the mosaicism percentage and the run quality. Beneath it, the record holds one row per chromosome per embryo, each with a measured copy number and its own call, so a full twenty-four-chromosome profile is reconstructable for any embryo months or years later. A third level captures sub-chromosomal imbalances by cytoband, each flagged as a gain, a loss or normal and sized in megabases, which is what a structural-rearrangement carrier's report actually needs. These matrices are held in the data model and exposed through the API today; there is no dedicated data-entry screen for them yet.

• Embryo ploidy call: euploid, aneuploid, mosaic or no result
• Copy number recorded per chromosome, 1 to 22, X and Y
• Per-chromosome flag: normal, gain, loss or mosaic
• Segmental region, gain or loss, and size in megabases
• Mosaic percentage and run quality held on the parent record

Cleavage-stage biopsy, scored nucleus by nucleus

Blastomere biopsy has its own result structure, because a single cleavage-stage cell is not always a single nucleus. The record holds the overall blastomere result, then a per-marker table of the two observed alleles with a per-marker interpretation, and separately a per-nucleus table numbering each nucleus in the biopsied cell with its observed signal pattern and its own call. That separation is deliberate: it preserves the difference between a genotype read and an interphase signal count, which a single free-text result field destroys. The system models these levels; no dedicated screen has been built for them yet.

Single-gene disease and saviour-sibling HLA typing

PGT-M and PGT-HLA share one structure, because in practice they share one workflow. The record names the disease, the causative gene and the mutation class, then carries the HLA-matching outcome and the affected, carrier or normal disease call with a narrative interpretation. Under it sits the analysis that makes an indirect test defensible: a per-marker table holding the mother's allele, the father's allele and the embryo's allele side by side, so inheritance is followed by linkage rather than asserted. A generic allele session record covers the same genotyping done outside a PGT run, for test set-up or family haplotyping, calling each embryo carrier, affected, normal or unknown. A separate per-embryo roll-up then consolidates the verdict for transfer ranking, carrying the overall result, the ploidy, the disease status, an explicit HLA-match flag and a numeric transfer priority.

The assays around PGT, not only the PGT itself

A reproductive genetics service is more than embryo testing, and the record set reflects that. Classical FISH cytogenetics on patient cells records the sample, the probe panel and the referral laboratory with a per-chromosome signal count and a monosomy, trisomy or nullisomy interpretation. Sperm FISH assesses the male partner's aneuploidy rate, holding the number of sperm scored and the probe panel with per-chromosome disomy, nullisomy and diploidy percentages. QF-PCR stores the marker, its allele peak sizes and the result, the rapid route to chromosome 13, 18, 21, X and Y aneuploidy detection and to a maternal-contamination check. Y-chromosome microdeletion screening tests the AZFa, AZFb and AZFc regions and SRY individually rather than as one verdict. Thrombophilia genotyping gives Factor V Leiden, prothrombin G20210A, MTHFR C677T and A1298C, PAI-1 4G/5G and Factor XIII their own columns, each normal, heterozygous or homozygous, with a JSON bucket for markers beyond the fixed panel. Fragile-X sizing holds both alleles' CGG repeat counts with the AGG interruption count and the normal, intermediate, premutation or full-mutation band.

Identity, confirmation and sign-off

A genetic call is only as good as the certainty that the DNA came from the right place. The DNA identification record covers identity confirmation, maternal-contamination checking and parentage, with a per-locus STR genotype table holding both alleles at each locus, the fingerprint itself. Separately, the lab's formal confirmation report is stored against the PGT header with its full narrative, its external laboratory reference and the user who confirmed it, keeping the written confirmation distinct from the result data. A genetic report approval record then captures who signed off, when, and whether the approval was clinical, genetic or administrative. Access control carries a dedicated Approve permission on genetic reports, and the platform's approval engine, with templated chains, SLA deadlines, delegation and an append-only decision log, is built and surfaced through admin screens and a personal approvals inbox. Automatic routing of every clinical event into those chains is still being completed.