Condition Database
107 Genetic Conditions,
Biologically Validated
Every condition is simulated with reference-backed hg38 sequences, aligned with BWA, and validated through category-specific detection pipelines at 95%+ alignment rate. Validated for synthetic data generation — not yet validated in clinical patient samples.
Aneuploidy
14 Aneuploidy Conditions
Whole chromosome copy number changes detectable via coverage-based z-scores. Includes common trisomies, sex chromosome aneuploidies, rare autosomal trisomies, and complex karyotypes.
| Condition | Gene / Region | Metric | Prevalence | Notes |
|---|---|---|---|---|
| Trisomy 21 OMIM | chr21 | z = 7.66 | 1 in 700 | Most common viable autosomal trisomy |
| Trisomy 18 OMIM | chr18 | z = 5.53 | 1 in 5,000 | Edwards syndrome |
| Trisomy 13 OMIM | chr13 | z = 7.48 | 1 in 16,000 | Patau syndrome |
| 45,X (Turner syndrome) OMIM | chrX | z = -6.46 | 1 in 2,500 | Monosomy X |
| 47,XXY (Klinefelter) OMIM | chrX | z = 2.68 | 1 in 660 | Sex chromosome aneuploidy |
| 47,XXX (Triple X) OMIM | chrX | z = 5.89 | 1 in 1,000 | Sex chromosome aneuploidy |
| 47,XYY OMIM | chrY | z = 9.47 | 1 in 1,000 | Sex chromosome aneuploidy |
| Trisomy 8 OMIM | chr8 | z = 3.22 | Rare | Often mosaic |
| Trisomy 9 OMIM | chr9 | z = 8.36 | Rare | Rare autosomal trisomy |
| Trisomy 10 | chr10 | z = 5.36 | Very rare | Rare autosomal trisomy |
| Trisomy 16 | chr16 | z = 6.98 | Rare | Most common trisomy in miscarriage |
| Trisomy 22 OMIM | chr22 | z = 4.12 | Rare | Rare autosomal trisomy |
| Triploidy (69,XXX/XXY) | genome-wide | z = multi-chr | 1 in 10,000 | Complete extra haploid set |
| 48,XXYY syndrome | chrX/chrY | z = 2.69 | 1 in 18,000 | Complex sex chromosome aneuploidy |
Microdeletion
24 Microdeletion Conditions
Sub-chromosomal deletions detected via regional log2 coverage ratios with Poisson statistical testing. GC-normalised for accurate signal quantification across deletions from 450 kb to 21 Mb.
| Condition | Gene / Region | Metric | Prevalence | Notes |
|---|---|---|---|---|
| DiGeorge syndrome (3.0 Mb A-D) OMIM | 22q11.2 | log2 = -0.11 | 1 in 4,000 | 3.0 Mb deletion, ~85-90% of cases. LCR22A-D breakpoints. GC-rich region with mappability-aware modelling. |
| DiGeorge syndrome (1.5 Mb A-B) OMIM | 22q11.2 | log2 = -0.07 | 1 in 4,000 | 1.5 Mb deletion, ~5-8% of cases. LCR22A-B breakpoints. |
| DiGeorge syndrome (2.0 Mb A-C) OMIM | 22q11.2 | log2 = -0.09 | 1 in 4,000 | 2.0 Mb deletion, ~2-3% of cases. LCR22A-C breakpoints. |
| Cri du Chat OMIM | 5p | log2 = -0.10 | 1 in 50,000 | Terminal 5p deletion |
| Williams syndrome OMIM | 7q11.23 | log2 = -0.07 | 1 in 10,000 | 1.4 Mb ELN region |
| Prader-Willi syndrome OMIM | 15q11.2 | log2 = -0.09 | 1 in 15,000 | Paternal deletion |
| Angelman syndrome OMIM | 15q11.2 | log2 = -0.09 | 1 in 15,000 | Maternal deletion |
| Wolf-Hirschhorn OMIM | 4p16.3 | log2 = -0.14 | 1 in 50,000 | Terminal 4p deletion |
| Smith-Magenis OMIM | 17p11.2 | log2 = -0.11 | 1 in 25,000 | RAI1 region |
| Jacobsen syndrome OMIM | 11q24 | log2 = -0.12 | 1 in 100,000 | Terminal 11q deletion, 21 Mb |
| Langer-Giedion OMIM | 8q24 | log2 = -0.15 | Rare | TRPS1/EXT1 region |
| 1p36 deletion OMIM | 1p36 | log2 = -0.11 | 1 in 5,000 | Most common terminal deletion |
| 16p11.2 deletion OMIM | 16p11.2 | log2 = -0.43 | 1 in 2,000 | Autism-associated, 600 kb |
| 2q37 deletion OMIM | 2q37 | log2 = -0.11 | Rare | Brachydactyly-mental retardation |
| 3q29 deletion OMIM | 3q29 | log2 = -0.24 | 1 in 30,000 | Psychiatric phenotype |
| Miller-Dieker syndrome OMIM | 17p13.3 | log2 = -0.12 | 1 in 100,000 | LIS1/YWHAE, lissencephaly |
| Koolen-de Vries syndrome OMIM | 17q21.31 | log2 = -0.10 | 1 in 55,000 | KANSL1, 624 kb |
| 15q11.2 BP1-BP2 (Burnside-Butler) OMIM | 15q11.2 | log2 = -0.08 | 1 in 200 | NIPA1, 452 kb, incomplete penetrance |
| 15q13.3 deletion OMIM | 15q13.3 | log2 = -0.10 | 1 in 40,000 | CHRNA7, epilepsy risk |
| 16p12.2 deletion OMIM | 16p12.2 | log2 = -0.09 | Rare | CDR2/EEF2K, 500 kb |
| Rubinstein-Taybi syndrome OMIM | 16p13.3 | log2 = -0.11 | 1 in 125,000 | CREBBP, 3.75 Mb |
| Glass syndrome OMIM | 2q33.1 | log2 = -0.13 | Rare | SATB2, 8.1 Mb |
| NRXN1 deletion OMIM | 2p16.3 | log2 = -0.10 | Rare | Autism/schizophrenia risk, 1.1 Mb |
| X-linked ichthyosis OMIM | Xp22.31 | log2 = -0.11 | 1 in 6,000 males | STS deletion, 1.7 Mb |
Microduplication
4 Microduplication Conditions
Sub-chromosomal duplications detected via positive regional log2 coverage ratios. Inverse of microdeletion detection with increased coverage in the duplicated region.
| Condition | Gene / Region | Metric | Prevalence | Notes |
|---|---|---|---|---|
| 22q11.2 duplication OMIM | 22q11.2 | log2 = +0.10 | 1 in 700 | 2.6 Mb, variable phenotype |
| 7q11.23 duplication OMIM | 7q11.23 | log2 = +0.08 | Rare | Reciprocal of Williams deletion |
| Potocki-Lupski syndrome OMIM | 17p11.2 | log2 = +0.10 | 1 in 25,000 | Reciprocal of Smith-Magenis |
| 16p11.2 duplication OMIM | 16p11.2 | log2 = +0.09 | 1 in 2,000 | Reciprocal of 16p11.2 deletion |
Monogenic
49 Monogenic Conditions
Single-gene disorders detected via variant allele frequency (VAF) in cell-free DNA. Includes SNVs, small indels, and structural deletions. Covers haemoglobinopathies, skeletal dysplasias, RASopathies, connective tissue disorders, neurodevelopmental conditions, and treatable metabolic diseases.
| Condition | Gene / Region | Metric | Prevalence | Notes |
|---|---|---|---|---|
| Sickle Cell Anemia OMIM | HBB | VAF = 0.070 | 1 in 500 (AFR) | E6V missense |
| Cystic Fibrosis OMIM | CFTR | VAF = 0.055 | 1 in 2,500 (EUR) | F508del |
| Beta-thalassemia OMIM | HBB | VAF = 0.095 | 1 in 100,000 | Splice site variant |
| Alpha-thalassemia OMIM | HBA1/HBA2 | log2 = -0.24 | 1 in 10,000 | SEA deletion (structural) |
| Spinal Muscular Atrophy OMIM | SMN1 | log2 = -0.15 | 1 in 10,000 | Exon 7 deletion (structural) |
| Tay-Sachs Disease OMIM | HEXA | VAF = 0.100 | 1 in 3,500 (AJ) | 1278insTATC |
| Achondroplasia OMIM | FGFR3 | VAF = 0.070 | 1 in 15,000 | G380R de novo |
| Pfeiffer syndrome OMIM | FGFR1 | VAF = 0.065 | 1 in 100,000 | R661X de novo |
| Thanatophoric dysplasia I OMIM | FGFR3 | VAF = 0.070 | 1 in 60,000 | R248C / S249C de novo |
| Hypochondroplasia OMIM | FGFR3 | VAF = 0.068 | 1 in 15,000 | N540K missense |
| Osteogenesis imperfecta (COL1A1) OMIM | COL1A1 | VAF = 0.072 | 1 in 15,000 | Splice variant, AD |
| Osteogenesis imperfecta (COL1A2) OMIM | COL1A2 | VAF = 0.070 | 1 in 15,000 | Splice variant, AD |
| Stickler syndrome OMIM | COL2A1 | VAF = 0.068 | 1 in 7,500 | G504S missense |
| Noonan syndrome (PTPN11) OMIM | PTPN11 | VAF = 0.075 | 1 in 2,500 | N308D missense |
| Noonan syndrome (RAF1) OMIM | RAF1 | VAF = 0.070 | Rare | S257L, cardiac phenotype |
| Noonan syndrome (KRAS) OMIM | KRAS | VAF = 0.065 | Rare | G12C de novo |
| Costello syndrome OMIM | HRAS | VAF = 0.072 | 1 in 300,000 | G13D de novo, RASopathy |
| CFC syndrome OMIM | BRAF | VAF = 0.068 | 1 in 810,000 | Q257R de novo, RASopathy |
| Marfan syndrome OMIM | FBN1 | VAF = 0.065 | 1 in 5,000 | C1039Y missense |
| Neurofibromatosis type 1 OMIM | NF1 | VAF = 0.070 | 1 in 3,000 | R1947X nonsense |
| Rett syndrome OMIM | MECP2 | VAF = 0.085 | 1 in 10,000 | R168X, X-linked de novo |
| Dravet syndrome OMIM | SCN1A | VAF = 0.070 | 1 in 15,000 | F1846L de novo |
| DYRK1A-related ID OMIM | DYRK1A | VAF = 0.068 | Rare | R255X de novo |
| Coffin-Siris syndrome OMIM | ARID1B | VAF = 0.072 | Rare | R1990X de novo |
| KAT6A syndrome OMIM | KAT6A | VAF = 0.070 | Rare | R1129X de novo |
| Duchenne Muscular Dystrophy OMIM | DMD | log2 = -0.28 | 1 in 3,500 males | Exon 45 deletion (structural) |
| Hemophilia A OMIM | F8 | VAF = 0.080 | 1 in 5,000 males | Intron 22 inversion |
| Tuberous sclerosis OMIM | TSC2 | VAF = 0.090 | 1 in 6,000 | R1743Q missense |
| Cornelia de Lange OMIM | NIPBL | VAF = 0.065 | 1 in 10,000 | R2298X de novo |
| Treacher Collins OMIM | TCOF1 | VAF = 0.075 | 1 in 50,000 | K1060X nonsense |
| CHARGE syndrome OMIM | CHD7 | VAF = 0.080 | 1 in 10,000 | R2178X de novo |
| Smith-Lemli-Opitz OMIM | DHCR7 | VAF = 0.060 | 1 in 20,000 | Splice site, AR |
| Phenylketonuria OMIM | PAH | VAF = 0.070 | 1 in 10,000 | R408W missense, treatable |
| Gaucher Disease OMIM | GBA | VAF = 0.095 | 1 in 40,000 | N370S, Ashkenazi founder |
| Canavan Disease OMIM | ASPA | VAF = 0.075 | 1 in 6,400 (AJ) | E285A missense |
| Bloom syndrome OMIM | BLM | VAF = 1.000 | 1 in 48,000 (AJ) | blmAsh deletion |
| Niemann-Pick type C OMIM | NPC1 | VAF = 0.080 | 1 in 120,000 | I1061T missense |
| Fanconi Anemia OMIM | FANCA | VAF = 0.055 | 1 in 160,000 | E1439K splice variant |
| Mucopolysaccharidosis I OMIM | IDUA | VAF = 0.095 | 1 in 100,000 | W402X nonsense |
| Alport syndrome OMIM | COL4A5 | VAF = 1.000 | 1 in 50,000 | G325R, X-linked |
| Polycystic Kidney Disease OMIM | PKHD1 | VAF = 0.040 | 1 in 20,000 | T36M missense, ARPKD |
| Pompe Disease OMIM | GAA | VAF = 0.065 | 1 in 40,000 | E176RfsX45, treatable (ERT) |
| Adrenoleukodystrophy OMIM | ABCD1 | VAF = 0.070 | 1 in 17,000 | Q472RfsX83, X-linked, treatable |
| Galactosaemia OMIM | GALT | VAF = 0.075 | 1 in 60,000 | Q188R, treatable (diet) |
| Maple Syrup Urine Disease OMIM | BCKDHA | VAF = 0.068 | 1 in 185,000 | Y438N, treatable (diet) |
| MCADD OMIM | ACADM | VAF = 0.072 | 1 in 15,000 | K329E, treatable (diet) |
| Biotinidase Deficiency OMIM | BTD | VAF = 0.070 | 1 in 60,000 | R538C, treatable (biotin) |
| Congenital Adrenal Hyperplasia OMIM | CYP21A2 | VAF = 0.065 | 1 in 15,000 | Q319X, treatable (cortisol) |
| Alagille Syndrome OMIM | JAG1 | VAF = 0.068 | 1 in 30,000 | C1085Y, AD |
Oncology Hotspots
10 Oncology Hotspots Conditions
Somatic driver mutations for liquid biopsy validation. VAF represents tumour fraction rather than foetal fraction. Covers the most clinically actionable mutations across NSCLC, CRC, melanoma, breast, and pan-cancer.
| Condition | Gene / Region | Metric | Prevalence | Notes |
|---|---|---|---|---|
| EGFR L858R OMIM | EGFR | VAF = 0.070 | Common in NSCLC | Lung cancer driver, TKI-sensitive |
| EGFR T790M OMIM | EGFR | VAF = 0.065 | NSCLC resistance | Third-gen TKI target |
| KRAS G12D OMIM | KRAS | VAF = 0.072 | CRC/Pancreatic | Most common KRAS mutation |
| KRAS G12V OMIM | KRAS | VAF = 0.070 | CRC/Pancreatic | Second most common KRAS |
| BRAF V600E OMIM | BRAF | VAF = 0.075 | Melanoma/CRC | BRAF inhibitor target |
| PIK3CA H1047R OMIM | PIK3CA | VAF = 0.068 | Breast cancer | Kinase domain hotspot |
| PIK3CA E545K OMIM | PIK3CA | VAF = 0.070 | Breast cancer | Helical domain hotspot |
| TP53 R273C OMIM | TP53 | VAF = 0.072 | Pan-cancer | Contact mutant, GOF |
| TP53 R248W OMIM | TP53 | VAF = 0.068 | Pan-cancer | Structural mutant, GOF |
| NRAS Q61R OMIM | NRAS | VAF = 0.070 | Melanoma/AML | RAS pathway oncogene |
Repeat Expansion
4 Repeat Expansion Conditions
Trinucleotide repeat expansions detected via repeat motif counting in aligned reads and soft-clipped bases. Targeted fragment generation ensures coverage at the repeat locus.
| Condition | Gene / Region | Metric | Prevalence | Notes |
|---|---|---|---|---|
| Fragile X syndrome OMIM | FMR1 | 190 CGG repeats | 1 in 4,000 males | CGG expansion (>200 repeats) |
| Huntington Disease OMIM | HTT | 194 CAG repeats | 1 in 10,000 | CAG expansion (>36 repeats) |
| Myotonic Dystrophy Type 1 OMIM | DMPK | 80 CTG repeats | 1 in 8,000 | CTG expansion (>50 repeats) |
| Spinocerebellar Ataxia Type 1 OMIM | ATXN1 | 55 CAG repeats | 1 in 100,000 | CAG expansion (>39 repeats) |
Imprinting
2 Imprinting Conditions
Imprinting disorders detected via regional coverage changes and fragment size distribution shifts at imprinted loci.
Methodology
Validation Pipeline
Generate
Reference-backed fragments from hg38 with condition-specific signals: coverage modifiers, variant injection, or repeat expansion at the correct genomic locus.
Align
BWA-MEM alignment against GRCh38 reference. All conditions achieve >95% mapping rate, confirming biological plausibility of generated sequences.
Detect
Category-specific detection: z-scores for aneuploidies, log2 ratios with Poisson tests for microdeletions and microduplications, VAF via pileup for monogenics and oncology hotspots, motif counting for repeat expansions.
Validate
GC-normalised metrics compared against detection thresholds. All 107 conditions produce the expected signal at 15% foetal fraction.
Generate Synthetic Data for Any Condition
All 107 conditions are available for synthetic cfDNA generation. Custom fetal fractions, fragment depths, and multi-condition samples supported.