Enabling Informed Clinical Decisions with Deep InsightsRoutine Multi-gene Testing for Inherited Neuromuscular Disorders

Introduction – Multi-gene Testing for Inherited Neuromuscular Disorders

Inherited Neuromuscular Disorders (NMDs) are a complex and heterogeneous group of disorders with the genetic cause of the disease remaining unknown for many patients. Conventional gene-by-gene molecular diagnostic approaches (single-gene testing) do not provide adequate information to accurately diagnose a case with complex phenotypes and unknown mutations.

Multi-gene testing using Next-Generation Sequencing (NGS) can provide accurate, and rapid clinical diagnosis for complex and heterogeneous neuromuscular disorders, at a cost lesser than conventional single-gene testing.

Highlights of NGS Testing for Neuromuscular Disorders

• High clinical utility for improved disease management and treatment decisions.

• Molecular confirmation of a clinical diagnosis.

• Recurrence risk assessment for future pregnancies and prenatal testing after confirmation of diagnosis.

• Aids in differential diagnosis.

• Facilitates carrier testing (for autosomal recessive disorders).

• Identification of at-risk family members.

• Accurate information for comprehensive genetic counseling.

Muscular dystrophies (MD) are a group of muscle diseases characterized by muscle weakness and wasting that is usually progressive, with continuous degeneration/regeneration of muscle fibers. Serum creatine kinase level is usually elevated. In this test, MD has been further classified as: collagen type VI-related disorders, dystroglycanopathy, dystrophinopathy, Emery-Dreifuss MD and limb-girdle MD depending on the underlying genetic cause.

Dystonia is a neuromuscular disorder characterized by involuntary muscle contractions that cause slow repetitive movements or abnormal postures and may have other neurologic features. Dystonia can affect only one muscle, groups of muscles or muscles throughout the body. In this test, dystonia has been further classified as: focal and generalized dystonia, complex dystonia and parkinsonism associated dystonia.

Ataxia is a term for a group of disorders that affect coordination of muscle movements that includes gait (movement of limbs) abnormality. Ataxia is a non-specific clinical manifestation implying dysfunction of the parts of the nervous system that coordinate movement, such as the cerebellum. The clinical manifestations are seen in childhood itself in many cases, and may result from one or a combination of dysfunction of the cerebellar systems, lesions in the spinal cord or peripheral sensory loss. In this test, ataxia has been further classified as: cerebellar ataxia, spinocerebellar ataxia, episodic ataxia, spastic paraplegia associated ataxia, neuronal ceroid lipofuscinosis, mitochondrial disorders associated ataxia and epilepsy associated ataxia.

Congenital myopathy refers to a genetically and clinically heterogeneous group of progressive disorders characterized by muscle weakness and hypotonia at birth or in infancy. Typically, an infant with a congenital myopathy will be "floppy," have difficulty breathing or feeding, and will lag behind other babies in meeting normal developmental milestones such as turning over or sitting up. In this test, congenital myopathy has been further classified as: nemaline myopathy, distal myopathy, myofibrillar myopathy, centronuclear myopathy, Bethlem myopathy and congenital fiber-type disproportion.

Hereditary spastic paraplegia (HSP) is a group of inherited neuromuscular disorders that cause weakness and stiffness of the lower part of the body. HSP is a progressive condition and is also known as familial spastic paraparesis or Strümpell-Lorrain syndrome.

Neuropathies are a group of disorders affecting the peripheral nervous system. The symptoms of hereditary neuropathies may be congenital or appear in adulthood. Variable expression of clinical features is seen among different family members, with some family members being more severely affected than others. In this test, neuropathies have been further classified as: hereditary motor and sensory neuropathy, Charcot-Marie-Tooth disease, peripheral neuropathy, axonal neuropathy, Dejerine-Sottas disease, polyneuropathy, amyloidosis associated neuropathy and ataxia associated neuropathy.

Amyotrophic Lateral Sclerosis is a progressive neurodegenerative disease involving the upper (UMN) and lower motor neurons (LMN). Symptoms of UMN include hyperreflexia (overactive or overresponsive reflexes), increased muscle tone, and weakness. LMN signs include weakness, muscle wasting, hyporeflexia (below normal or absent reflexes), muscle cramps and involuntary twitching of muscles. The presentation varies amongst individuals.

Clinical Indications of Disorders Covered in the Neuromuscular Test

Muscular Dystrophies

Disorders Description

Dystonia

Congenital Myopathy

Spastic Paraplegia

Neuropathies

Amyotrophic Lateral Sclerosis

Ataxia

Can the Neuromuscular TestBe Offered for Prenatal Diagnosis?

• Patient with clinical features (hypotonia, hypertonia, spasticity, increased CPK levels, movement disorders) indicative of one of the 7 neuromuscular conditions.

• Carrier testing for couples who have lost a child whose clinical features were indicative of one of these disorders.

• Single gene test or MLPA tests have returned inconclusive; to rule out point mutations.

• For differential diagnosis.

Who to Test?

Benefits of NGS/Multi-gene Testing for Neuromuscular Disorders

1. Rapid turnaround time and cost-effectiveness.

2. Unprecedented sequencing speed by massive parallel sequencing technology and

ability to look at many genes at the same time.

3. NGS can detect different types of mutations in the DNA sequence, such as

SNVs, indels and large deletions or duplications.

4. Diagnosis of complex phenotypes.

This test is not offered directly for prenatal diagnosis. However, a prenatal diagnosis can be offered based on the identified variation(s) in the proband's sample or after carrier testing in the parents.

Neuromuscular Test Genes & Test Selection

COL6A1, COL6A2, COL6A3, COL12A1

DMD, SGCA, SGCB

B3GNT1, FKRP*, FKTN, ISPD*, LARGE, POMGNT1, POMGNT2, POMT1, POMT2

EMD*, FHL1, LAMP2, SUN2, SYNE1, SYNE2, TMEM43

ANO5, CAPN3, CAV3*, DES*, DNAJB6, DYSF, EMD*, FHL1, FKRP*, FKTN, GAA, LAMA2, MYOT, PLEC, POMGNT1, POMT1, POMT2, SGCA, SGCB, SGCD, SGCG, TCAP, TRIM32, TTN

ANO5, BAG3, BIN1, CHKB, CLCN1, DAG1, DES*, DPM1, DPM3, DYSF, FKTN, FRG1*, GAA, ITGA7, MYOT, PABPN1*, PHKA1, PLEC, POMGNT1, POMT2, PYGM, SCN4A, SEPN1*, TTN

DRD5, PRKRA, THAP1, TOR1A

ARSA, ATP7B, AUH, BCS1L, C19orf12, COX10, COX15, CP, DCAF17, FA2H, FOXRED1, FTL, GCDH, MECP2*, MTFMT, NDUFA10*, NDUFA12, NDUFA2, NDUFA9, NDUFAF2, NDUFAF6, NDUFS1, NDUFS3, NDUFS4, NDUFS7, NDUFS8, NPC1, NPC2, PANK2*, PARK2, PDGFB, PDHX*, PLA2G6, SDHA, SUCLA2, SURF1*, VPS13A, WDR45, XK

ATP13A2, ATP1A3, GCH1*, PRKRA, SLC6A3, SPR, TH

ACTB, ADCY5*, ARFGEF2, ATM*, ATP1A3, BCAP31, DRD2, FA2H, PNKD, PRRT2, SCP2, SLC2A1, SLC30A10, SUCLA2, TIMM8A

ATCAY, ATP1A3, ATP8A2, CA8, CACNA1A, CLN6*, CYP27A1, DNMT1, FASTKD2, KIAA0226, OPA3, PAX6, PLEKHG4, SCN8A, VLDLR, WDR81, ZNF592

ADCK3, AFG3L2*, ANO10, C10orf2, CA8, CACNA1A, CCDC88C, ELOVL4, FGF14, GJB1, GRM1, IFRD1, ITPR1, KIAA0226, PDYN, PRKCG, SETX, SPTBN2, SYNE1, SYT14, TDP1, TGM6, TPP1, TRPC3, TTBK2, WWOX

CACNA1A, CACNB4, KCNA1, SLC1A3

Disorders Gene listDisorders subtype Number of Genes

Collagen type VI-relateddisorders

Muscular dystrophy

Dystonia

Ataxia

Dystroglycanopathy

4

9

Dystrophinopathy

Emery-Dreifuss musculardystrophy

Focal and generalized dystonia

Complex dystonia

Parkinsonism associated dystonia

Cerebellar ataxia

Spinocerebellar ataxia‡

Episodic ataxia

Others

3

7

Limb-girdle musculardystrophy 24

Others 24

4

39

7

15

17

26

4

6

4

6

6

48

7

7

5

5

4

KIF1A, PNPLA6, SPAST, SPG7*, ZFYVE26, ZFYVE27

COQ2, COQ9*, NDUFS7, NUBPL, PDSS2, SDHA

CLN5*, CLN6*, KCTD7*, TPP1

GOSR2, KCTD7*, MTTP, POLG, PRICKLE1*, WWOX

Spastic paraplegiaassociated ataxia

Neuronal ceroidlipofuscinosis

Mitochondrial disordersassociated ataxia

Epilepsy associated ataxia

Others ABCB7, ABHD12, AFG3L2*, APTX, ATM*, ATP1A3, C10orf2, CACNA1A, COQ2, CYP27A1, DARS2, DNAJC19, FLVCR1*, FMR1*, FXN*, GJB1, KCNJ10, KCTD7*, MECP2*, MRE11A, MTPAP, MTTP, NKX2-1*, NPC1, NPC2, OPA1, PEX10*, PEX16, PEX2, PEX7, PHYH, PIK3R5, PMM2, PNKP, PNPLA6, POLG, POLR3A, POLR3B, PRX*, PSEN1, RNF170, SACS, SCN1A, SIL1, SRD5A3, TTPA*, VLDLR, WFS1

ACTA1, CFL2, KBTBD13*, NEB*, TNNT1, TPM2, TPM3Congenitalmyopathy

Nemaline myopathy

CAV3*, DYSF, FLNC, KLHL9, MATR3, MYH7, MYH14

BAG3, CRYAB, FLNC, LDB3*, MYOT

BIN1, DNM2*, MTMR14, MYF6, TTN

Distal myopathy

Myofibrillar myopathy

Centronuclear myopathy

COL6A1, COL6A2, COL6A3, COL12A1Bethlem myopathy

How to Select a Test for Your Patient?

Disorders Gene listDisorders subtype Number of Genes

5

39

47

42

50

12

9

4

8

3

5

42

34

ACTA1, RYR1, SEPN1*, TPM2, TPM3Congenital fiber-typedisproportion

Congenitalmyopathy

ACTA1, ANO5, ATP2A1, CAV3*, CHKB, CNTN1, COL6A1, COL6A2, COL6A3, DES*, FHL1, FKBP14, GBE1, GFER*, GNE, HRAS, ISCU, ITGA7, LAMP2, MEGF10, MTM1, MYH14, MYH2, MYH7, MYOT, OPA1, ORAI1, PABPN1*, PNPLA2*, PUS1, RYR1, SEPN1*, SIL1, TAZ, TPM2, TPM3, TTN, VCP, YARS2

Others

ABCD1, ALDH18A1, ALS2, AP4B1, AP4E1, AP4M1, AP4S1*, AP5Z1, ATL1, ATP2B4, BSCL2, C12orf65, C19orf12, CCT5, CYP7B1, ELOVL4, ENTPD1, ERLIN2, EXOSC3, FA2H, GAD1, GBA, HSPD1, IFIH1, KDM5C , KIAA0196, KIF1A, KIF5A, L1CAM, PLP1, PNPLA6, PSEN1, RAB3GAP2, REEP1, RTN2, SACS, SLC16A2, SLC33A1, SPAST, SPG11, SPG20, SPG21, SPG7*, VCP, ZFYVE26, ZFYVE27

AARS, ATL1, ATP7A, BSCL2, CCT5, DCTN1, DNMT1, FAM134B, GARS, GJB1, HADHB , HK1, HSPB1*, HSPB3, HSPB8, IFRD1, IGHMBP2, IKBKAP, KIF1A, MFN2, MPZ, MTMR2, NDRG1, NEFL, NGF, NTRK1, PHYH, PRX*, RAB7A, REEP1, SACS, SCN9A, SETX, SH3TC2, SLC12A6, SLC5A7, SPTLC2, SYT2, TRPV4, VRK1, WNK1

AARS, AIFM1, ARHGEF10, BSCL2, CTDP1*, DNAJB2, DNM2*, DYNC1H1, EGR2*, FBLN5, FGD4, FIG4, GAN, GARS, GDAP1, GJB1, HARS, HK1, HOXD10, HSPB1*, HSPB8, IGHMBP2, INF2, KARS, KIF1B, KIF5A, LITAF, LRSAM1, MED25, MFN2, MPZ, MTMR2, NDRG1, NEFL, PMP22, PRPS1, PRX*, RAB7A, REEP1, SBF2, SETX, SH3TC2, SLC12A6, SOX10, SPTLC2, SYT2, TRPV4, VCP, WNK1, YARS

AARS, ARHGEF10, GDAP1, GJB1, GJB3, KARS, MYH14, SCN10A, SLC12A6, SOX10, TRPV4, YARS

CD59, GAN, LRSAM1, MFN2, NEFL, SETX, TDP1, TRPV4, VRK1

EGR2*, MPZ, PMP22, PRX*

ABHD12, APOA1, CD59, GJB1, MCM3AP, SLC25A19*, TTR, TYMP

APOA1, TTR, TYMP

AFG3L2*, IFRD1, SACS, SETX, TDP1

AAAS, AARS, ABCD1, AP1S1, ARHGEF10, C10orf2, CTDP1*, DFNB59, DHH*, DIAPH3, DYNC1H1, EGR2*, FBLN5, GDAP1, GJB1, GLA, HADHB, IGHMBP2, MPZ, MTMR2, NTRK1, OPA1, OTOF, PMP22, PNPLA6, POLG, PRF1, PRPS1, PRX*, RPIA, SCN10A, SCN9A, SCP2, SH3TC2, SLC12A6, SLC25A19*, SNAP29, SOX10, SYT2, TSFM*, TTR, TYMP

ALS2, ANG, APEX1, C9orf72, CHGB*, CHMP2B*, DAO, DCTN1, ERBB4, FIG4, FUS, GRN, MATR3, OPTN, PARK7, PFN1, PON1, PON2, PON3, PSEN1, SETX, SIGMAR1*, SOD1, SPG11, SQSTM1*, TAF15, TARDBP, TBK1, TRPM2, TRPM7, UBQLN2, VAPB, VCP

Spastic paraplegia

Neuropathy

Amyotrophic lateralsclerosis

Footnote:*Genes having 85%-95% coverage. All other genes have >95% coverage in this test. Disclaimer: Gene coverage varies from sample to sample in the NGS runs.‡ Spinocerebellar ataxia caused due to repeat expansions in the gene, are not covered in this panel.

Spastic paraplegia

Hereditary motor andsensory neuropathy

Charcot-Marie-Toothdisease

Peripheral neuropathy

Axonal neuropathy

Dejerine-Sottas disease

Polyneuropathy

Amyloidosis associatedneuropathy

Ataxia associatedneuropathy

Others

Amyotrophic lateralsclerosis

Based on the clinical indications of the patient and family history, select one appropriate disorder type/disorder subtype from the list provided above.

Genetic Testing Process

Sample Requirements (any one of the following)

Turnaround Time (TAT)

Test Prescription

Provide prescription to your patient for testing.

Risk Assessment

Risk assessment (to identify the risk, based on patient’s family history).

Pre-test Genetic Counseling

Pre-test genetic counseling (pros and cons of the test will be explained to patient).

Sample Collection

The hospital or our product specialist collects sample from patient in kits provided by us. Sample is sent to our lab for processing.

DNA isolated from bloodSaliva in collection kits provided by Strand

Blood in EDTA (purple top tube)

Sample Processing & Analysis

Samples are processed through state-of-the art analysis, interpretation, and reporting platforms by our team of expert scientists.

Report

Receive your clinical report securely through email. The final results are delivered in an easy-to-read report containing actionable genomic variant information. Our genetic counselors are available to help you review the results and answer any questions you may have.

Post-test Genetic Counseling

Post-test counseling (the results of the report will be explained to the patient by the genetic counselor).

4-6 weeks from receipt of sample in the lab

About StrandA History of Innovative Genomic Research

Strand Life Sciences is a global genomic profiling company aimed at empowering cancer care and genetic testing for inherited diseases. Strand works with oncologists, pathologists, and community hospitals to enable faster clinical decision support for accurate molecular diagnosis, prognosis, therapy recommendations, and clinical trials. Strand’s central reference laboratories are located in Bangalore, India and Colorado, USA.

www.strandls.com

A Trusted Partner to Companies WorldwideFor 15 years, our genomics products and solutions have facilitated the work of leading researchers and medical geneticists in over 2,000 laboratories and 100 hospitals around the world.

2016 © Strand Life Sciences

Strand Center for Genomics & Personalized Medicine (A unit of Strand Life Sciences Pvt. Ltd.) UAS Alumni Association Building, Veterinary College Campus, Bellary Road, Hebbal, Bangalore – 560 024Phone: +91-80-2309-5252, support.strandx@strandls.com, www.strandcenters.com

SCG

PM-M

KTG

-000

63-V

2