Choosing the right genetic test is more important than choosing the biggest one. A well-targeted single-gene Sanger may have higher diagnostic yield than a broad NGS panel that doesn’t include the suspect gene; a multi-gene panel may have lower yield than the right repeat-expansion assay. This page is the decision framework — how to pick the right test for the clinical situation.

🔹 Bottom Line: When to Order Each Test

Three pre-test questions: (1) How narrow is the differential? (2) What variant type does the disease produce? (3) What is the testing goal — diagnosis, predictive, reproductive, treatment selection?
Narrow differential (single gene unambiguous) → single-gene Sanger ± del/dup.
Multiple genes in one category → multi-gene NGS panel.
Atypical / undifferentiated phenotype → trio WES (or singleton if parents unavailable).
After WES negative with persistent suspicion → WGS (where available) or directed reflex (long-read, RNA-seq).
Suspected repeat expansion → disease-specific repeat assay (NGS will miss).
Suspected mitochondrial disease → whole mtDNA + nuclear panel together; tissue choice matters.
Treatment-driven testing (SOD1 for tofersen, SMN1/SMN2 for SMA therapies, DMD for exon-skipping, TTR for hATTR, GLA for Fabry chaperone): order even when phenotype is provisional.

The Three Pre-Test Questions

1. How Narrow Is the Differential?

One gene unambiguously implicated → single-gene Sanger ± del/dup analysis.
- Examples: CADASIL → NOTCH3; Wilson disease → ATP7B; LHON → three primary mtDNA mutations; predictive testing for known familial variant.
Multiple plausible genes within a clinical category → multi-gene NGS panel.
- Examples: epilepsy panel, leukodystrophy panel, hereditary spastic paraplegia panel, CMT panel, LGMD panel, hereditary ataxia panel, dystonia panel, PD panel, FTD panel, ALS panel.
Atypical / multi-system / undifferentiated → trio WES (proband + parents) or singleton WES if parents unavailable. WGS if accessible.

2. What Variant Type Does the Disease Produce?

Match the assay to the biology — this is the most common error in neurogenetic workup.

Variant type	Required assay	Examples
SNV / small indel	Sequencing (Sanger, panel, WES, WGS)	CADASIL (NOTCH3 SNVs), Wilson (ATP7B SNVs), familial AD (PSEN1)
Repeat expansion	Disease-specific RP-PCR / Southern blot / long-read	HD (HTT CAG), FRDA (FXN GAA), SCAs, DM1/2, C9orf72, Kennedy, FXTAS
Large deletion / duplication	MLPA or microarray (often not detected reliably by NGS)	DMD/BMD (~70%), SMA (SMN1 exon 7 del), CMT1A (PMP22 dup), NF1 large dels
Mitochondrial heteroplasmic point mutation	mtDNA sequencing + tissue choice	MELAS (m.3243A>G), MERRF, LHON, NARP — blood often lower heteroplasmy than affected tissue
Large mtDNA deletion	Long-range PCR or Southern blot on muscle	Kearns-Sayre, CPEO — blood may be negative
Methylation defect	Methylation-specific PCR / MLPA / bisulfite	FXS full mutation, Prader-Willi, Angelman
Structural variant (inversion, translocation)	Microarray, WGS, or long-read	Some inherited cancer / dev delay syndromes
Somatic mosaic variant	Affected tissue (not blood) + sensitive sequencing	Sturge-Weber (GNAQ in brain/skin), mosaic NF1, mosaic TSC, mosaic MCAP

3. What Is the Testing Goal?

Diagnostic confirmation in a symptomatic patient → prioritize broad sensitivity; informed consent is brief.
Predictive / pre-symptomatic testing in an asymptomatic at-risk relative → narrow, specific testing for the known familial variant only. Formal pre-test genetic counseling is mandatory.
Reproductive risk assessment → carrier testing for known recessive disease in the family; consider expanded carrier screening before pregnancy.
Treatment selection → see the treatment-driven testing section below.

Decision Algorithm

Define the clinical phenotype as precisely as possible — the narrower the differential, the better the test choice.
List the candidate genes for the phenotype.
Identify the dominant variant type for those genes — point mutations? Expansions? Deletions? Mitochondrial?
Choose the test that detects that variant type:
- 1 gene + SNVs → single-gene Sanger ± del/dup.
- Several genes + SNVs → multi-gene NGS panel covering all candidates.
- Expansion mechanism → disease-specific repeat assay.
- Mitochondrial → whole mtDNA + nuclear panel; consider tissue.
- Atypical / multi-system → trio WES.
Verify the panel content — confirm the candidate genes are on the chosen panel.
Check for sponsored testing programs for the suspected disease (many free options exist).
Order, with appropriate counseling.

Common Decision Scenarios

Scenario 1: Adult-Onset Cerebellar Ataxia, Family History of Similar

First-line: SCA repeat-expansion panel (SCA1, 2, 3, 6, 7, 8, 10, 12, 17, DRPLA). Covers the most common dominant ataxias.
If negative: hereditary ataxia NGS panel for non-expansion SCAs and recessive ataxias.
If still negative + ataxia + neuropathy: long-read sequencing for RFC1 AAGGG (CANVAS).
If still negative: trio WES.

Scenario 2: Young Adult with TIA / Stroke + Subcortical White Matter Disease on MRI, Family History

First-line: NOTCH3 full-gene sequencing (CADASIL).
If negative: HTRA1 for CARASIL (recessive) or possibly autosomal-dominant HTRA1 small vessel disease; COL4A1/A2; small vessel disease NGS panel.
If positive NOTCH3 with VUS: skin biopsy for granular osmiophilic material (GOM).

Scenario 3: Adult-Onset Encephalopathy + Lactic Acidosis + Stroke-Like Episodes

First-line: m.3243A>G targeted testing (MELAS — covers ~80% of cases).
If negative + suspicion remains: whole mtDNA sequencing + nuclear mitochondrial NGS panel.
If blood is negative: muscle biopsy mtDNA + urine sediment mtDNA (higher heteroplasmy than blood).

Scenario 4: Adult with Asymmetric Distal Weakness + Foot Deformity + Family History

First-line: PMP22 duplication by MLPA (CMT1A — commonest).
If negative: CMT NGS panel (covers CMT1, CMT2, CMTX with GJB1, CMT4).
If still negative: trio WES.

Scenario 5: Asymptomatic Adult with Affected Parent (HD, Familial AD, FTD, ALS)

First step: refer for formal pre-test genetic counseling. Do not order testing in clinic on first visit.
Then: targeted testing for the known familial variant only.
The HD predictive testing protocol (multiple in-person counseling sessions, mental-health screening, post-test follow-up) is the model standard.

Scenario 6: ALS — Establish Diagnosis + Identify Treatment-Eligible Patients

Test in every ALS patient: ALS NGS panel (covering SOD1, FUS, TARDBP, TBK1, VCP, others) + C9orf72 hexanucleotide expansion (standard NGS misses this).
Treatment rationale: SOD1-positive patients are eligible for tofersen (FDA-approved 2023). Don’t wait to test SOD1 specifically — most ALS panels include it.

Scenario 7: Infant / Child with Suspected SMA

First-line: SMN1 exon 7 deletion analysis (MLPA or qPCR).
If SMN1 deletion not found but SMA strongly suspected: SMN1 sequencing for point variant on the second allele.
Critical for treatment: SMN2 copy number drives choice and prognosis (nusinersen / risdiplam / onasemnogene).

Scenario 8: Pediatric Epileptic Encephalopathy

First-line: comprehensive epilepsy NGS panel (>200 genes including SCN1A, SCN2A, SCN8A, KCNQ2, STXBP1, CDKL5, MECP2, GRIN2A/B).
If negative: trio WES (yield ~25–40% in epileptic encephalopathies).
For Dravet specifically: SCN1A sequencing + del/dup as a directed first-line if phenotype is classical.

Scenario 9: Atypical / Undifferentiated Multi-System Phenotype

Trio WES (proband + both parents) is the highest-yield single test.
If trio not possible: singleton WES; yield is somewhat lower.
If WES negative + suspicion remains: WGS (where available), RNA-seq reflex, long-read sequencing.
If still undiagnosed: request reanalysis every 2–3 years — new disease genes are identified continually.

Treatment-Driven Genetic Testing

Some genetic tests are ordered not (only) for diagnosis but to determine therapy eligibility. Order these when the result would change management even if the diagnosis is provisional.

Test	Therapy unlocked	When to order
SOD1 sequencing	Tofersen (anti-SOD1 ASO, FDA-approved 2023)	Any ALS patient; SOD1-positivity unlocks tofersen
SMN1 + SMN2 copy number	Nusinersen, risdiplam, onasemnogene	Any suspected SMA
DMD exon-specific analysis	Exon-skipping therapies (eteplirsen, golodirsen, viltolarsen, casimersen)	Confirmed DMD with deletion amenable to exon skipping
TTR sequencing	Patisiran, vutrisiran, inotersen, tafamidis	Any suspected hATTR amyloid polyneuropathy
GLA sequencing	Migalastat (chaperone therapy for amenable mutations)	Confirmed Fabry with amenable GLA mutation
FXN repeat sizing	Disease-modifying agents in development (omaveloxolone approved 2023)	Friedreich ataxia confirmation
CLN2 / TPP1	Cerliponase alfa (intracerebroventricular)	Late-infantile NCL
GAA sequencing	Alglucosidase alfa, cipaglucosidase alfa + miglustat	Confirmed Pompe disease
ABCD1 sequencing	Elivaldogene autotemcel (gene therapy for cerebral ALD)	Early cerebral X-ALD in pediatric patients
Newborn-screening positive enzyme tests	Various enzyme replacements (Pompe, MPS, Krabbe in some states)	Confirm gene → initiate therapy

🔹 Clinical Relevance: Order Treatment-Eligible Tests Early

For ALS, SMA, hATTR, Fabry, Pompe, and X-ALD, genetic testing is no longer just diagnostic — it determines whether a disease-modifying treatment is available. Order these tests even when the diagnosis is provisional: confirming SOD1-positive ALS unlocks tofersen, confirming hATTR unlocks patisiran or tafamidis, confirming Pompe unlocks enzyme replacement. The cost of testing is far less than the cost of delayed treatment.

What NOT to Order

Don’t order whole-exome as first-line when a targeted panel will cover the differential — yield is similar; cost is higher; insurance is less likely.
Don’t order an NGS panel for Huntington disease — standard NGS will not detect the CAG expansion.
Don’t order WES if you suspect a repeat expansion disorder — order the disease-specific repeat assay first.
Don’t order a single mtDNA mutation if the differential is broader — order whole mtDNA sequencing + nuclear panel.
Don’t order a karyotype if microarray is available — microarray detects much smaller CNVs.
Don’t order DTC (direct-to-consumer) tests as the primary diagnostic pathway — variable accuracy, limited variant interpretation, no counseling.
Don’t skip pre-test counseling for predictive testing in asymptomatic relatives.

Pitfalls and Pearls

Match the assay to the variant biology — most common error in neurogenetic workup.
Repeat expansions need disease-specific assays; NGS will miss them.
For X-linked diseases in females: enzyme activity can be normal — order gene sequencing.
Mitochondrial blood may be negative with positive muscle / urine — tissue heteroplasmy matters.
Trio WES > singleton WES when parents are available.
Pre-test counseling is mandatory for predictive testing.
Treatment-driven testing: order SOD1, SMN1/SMN2, DMD, TTR, GLA when the result changes therapy eligibility.
Sponsored testing programs are widely available — check before paying out-of-pocket.
Reanalysis of undiagnosed cases every 2–3 years often yields new diagnoses.

References

Rexach J, Lee H, Martinez-Agosto JA, et al. Clinical application of next-generation sequencing to the practice of neurology. Lancet Neurol. 2019;18(5):492-503.
Klein CJ, Foroud TM. Neurology individualized medicine: when to use next-generation sequencing panels. Mayo Clin Proc. 2017;92(2):292-305.
Miller DT, Adam MP, Aradhya S, et al. Chromosomal microarray as first-tier clinical diagnostic test. Am J Hum Genet. 2010;86(5):749-764.
Smith HS, Swint JM, Lalani SR, et al. Clinical application of genome and exome sequencing as a diagnostic tool for pediatric patients. Genet Med. 2019;21(1):3-16.