Topics 2 Block 1

Testing basics needed for insurance?

TIN for lab and doctor

ICD10 code

CPT billing code

Test code

Institutional billing

hospital bills insurance in aggregate

usually for inpatient

GT falls under the aggregate- need approval from the hospital

Insurance billing

most comm type outpt billing

cost of test billed to insurance

many factors in approval

Patient pay

pt pays lower cost directly to lab

only option if no insurance

Inpatient GT

every day they are in hospital

instituitional

in hospital doesn’t mean inpatient

when admitted to hospital=both inpt and outpt that day

Outpatient GT

any clinic

insurance or pt pay

Medicaid

every state

needs based up until 18

not for those born out of country

can extend to severe diability

pts do not get billed

lab can refuse to take medicaid

crossing state line is issue

Medicare

federal system

over 65 or younger w/ disability

supplemental plans- you can pay to add coverage

sets industry standard

Big payers

huge insurances

good coverage for basic tests

other factors like deductible and estimated OOP

always pre-auth

Marketplace insurance

affordable care act

states have their own and a federal one

not medicaid- pts pay for coverage

not great coverage

Harris health financial assistance program

avail to all living in harris w/ financial need

“gold card”

covers visit cost and blood work, not GT

NBS benefits

avail to all metabolic pts

covers formula, medical food, labs, visits

Special situations w/o insurance

• 1st month after baby born= under mom’s insurance

• preg loss=depends on week of preg, before 24=bill mom, after 24=depends on if there is breath=independent MRN

• pt death=no coverage after death only pt pay

Pre-authorize with a lab

benefits investigation

select test and lab preauths w/ insurance

does not guarantee coverage

can be done w/ mult labs at once

Pre-authorize with insurance

fill out the form

many labs provide generic forms

can also contact insuarnce directly

What to send with a pre-authorization

medical note signed by physician

the form

letter of medical necessity

any guidelines proving your point in the letter

Karyotype

Chromosome level- number, large rearrangements, large CNV

FISH

Presence/absence specific region, probe, can be rapid for aneuploidies and X/Y

Do when suspect: T13/T18, ambiguous genitalia, parental F/U studies

Panel

Specific set of conditions, high-ish confidence, free testing on some panels

Known variant testing

Cascade testing

Inherited vs de novo

Exome/Genome

Single nucleotide variants, CNVs, some triplet repeats depending on lab

CMA

CNVs- extra or missing pieces

areas of homozygosity

Methylation studies

Determines what is expressed in specific regions

Imprinting disorders (BWS, PWS, AS, RSS)

UPD

Peroxisome

In cytosol

Metabolism fatty acids and detoxification

Either proliferate by budding off of the ER or existing peroxisomes

Beta-oxidation, alpha-oxidation, etherphospholipid, glyoxylate detox

Can have disorder of peroxisome overall or of one of the steps in its function

Fatty Acid Beta-Oxidation

Very long chain fatty acids (longer than C26:0) that aren’t oxidized by mito

Oxidation of pristanic acid

Very long chain fatty acids

Part of brain mems, including myelin

Oxidized in peroxisome until small enough to do oxidation in mito for energy

High concentration in cytosol can cause further elongation, accumulation most severe in brain and adrenal gland= cell dysfunction and death

Etherphospholipid biosynthesis

Helps form platelet activating factor and plasmalogens- found in heart, skeletal, muscle, kidney, brain, RBCs

Enzymes in peroxisome= DHAPT (esterification) and ADHAPS (create alc from ether bond)

Etherphospholipids

Plasmologens most abundant

5-20% of phospholipids in mem

Antioxidant, mem struct mediator, storage polyunsaturated fats

Decrease seen in alzheimer’s and Parkinson’s

Fatty acid alpha-oxidation

Breakdown fatty acids with methyl group at 3 position (branched chain)

Only done in peroxisome

Breaks down phytanic acid into pristanic acid in diet

Check for phytanic acid on labs

Pristanic and phytanic acid

NEED the peroxisome to turn phytanic into pristanic because excess phytanic causes retinal degeneration and brain nerve damage

Glyoxylate detoxification

High levels glyoxylate can lead to increased oxalate in tissue=can precipitate into calcium oxalate salt, can accumulate in kidney

Enzyme=glyoxylate aminotransferase=only enzyme for this process in peroxisome, AGXT gene

Peroxisome Biogenesis Disorders

Peroxisome not forming correctly

Zellweger spectrum disorders

Rhizomelic chondrodysplasia punctata type 1

Single-peroxisomal-enzyme/transporter deficiencies

Specific protein problem

Zellweger Spectrum Disorders

peroxisome biosynth disorder (decreased peroxisomes)

13 PEX genes

AR

1 in 50,000

inborn error of metabolism

presentation: wide range- liver dysfunc, DD, neuro abnorm, adrenocortical dysfunc, hearing/vision

severity depends on severity of dysfunc, earlier=more severe

suspect when neuro pheno, brain anomalies, dysmorphic feats

NBS- very long chain fatty acids will be increased, phytanic/pristanic increased, plasmalogens decreased

WES/WGS

Zellweger geno-pheno and treatment

frameshift more severe

homo for PEX1 can be assoc w/ more or less severe depending on mut

tx: no cure, symptomatic, diets, monitor liver, hearing, feeding, vision, AEDS

Neonatal-infantile syndrome (Zellweger spectrum)

presentation- craniofacial dysmorphia (shallow orbit ridges, epicanthus, high arched palate, high forehead, external ear deform, small jaw, excess neck folds), profound neuro abnorm (hypotonia, seizures, retinal degen, hearing, malformed myelin)

prognosis=fatal in infancy, no developmental progression

Childhood presentation Zellweger

presentation: after birth but before 1yr, hypotonia, DD, seizure, abnorm brain, ocular

prognosis: may or may not walk/talk, progress degen white matter=loss previous skills, death by adolescence

Adolescent-Adult presentation Zellweger

presentation: mostmild, ocular/hearing, may or may not have dymorph facial feats, highly variable develop, primary adrenal insuff, neuro less comm

Rhizomelic chondrodysplasia punctata type 1

only part of peroxisome not working

PTS2

etherphospholipid synth and alpha-oxidation disrupted

PEX7, AR

proximal shortening of humerus and femur, congen contractures

punctate calcifications in cartilage

severe and apparent at birth or early infancy- rare to make it past 1st decade

skeletal, face feats (broad nasal bridge, high arched palate, dysplastic ears, small jaw), ID, respiratory

ocular, growth probs

Rhizomelic chondrodysplasia punctata type 1 testing and tx

biochem= RBC concen plasmogens, phytanic acid, very long chain fatty acid

GT=more accessible

cataract extract, PT, orthopedic, restrict phytanic acid, monitor growth and intell develop, feeding tube

challenging condition: severe ID, seizures in majority, decreased life expect (avg 2yrs)

Rhizomelic chondrodysplasia punctata types 2 and 3

GNAPT and AGPSaffects 1st and 2nd enzymes in etherphospholipid biosynth

similar pheno to type 1 but less severe

deficient erythrocyte plasmalogens, impaired synth etherphospho

no tx

Refsum disease-Adult

PHYH 90% (or PAHX), AR, rare

affects phytanoyl-CoA hydroxylase- defective alpha oxidation of phytanic acid=accum phytanic acid in cells

elevated phytanic levels

presentation= sympts by 20yr, anosmia and retinitis pigmentosa initially, slowly progressive (deafness, ataxia, polyneuropathy), ichthyosis, cardiac arrythmias

Refsum disease-Adult treatment

eliminate phytanic acid in food (dairy, beef, lamb, fish), slow improvement, deteriorating senses will not return but can stabalize

X-Linked Adrenoleukodystrophy

x-linked, ABCD1=ABC protein (helps transport very long chain fatty acids into peroxisome)

if not working=abnorm lipid concen in certain organs=demyelination of nerves and damage outer layer adrenal gland

1 in 21000 males

progressive, commonly see adrenoinsuff

comm pheno= chilhood cerebral form- severe but on NBS, adrenomyeloneuropathy, addisons’s disease w/o neuro

hetero females=typ asymp, rarely addisons

Childhood cerebral ALD

onset at 7yrs

resembles ADHD, progress impair cognition, behavior, vision, hearing, motor, probs w/ auditory discrim and spatial orientation

progress to vegetative state after 2yrs on avg ± 2 yrs

Adrenomyeloneuropathy

adult onset (late 20s-early 40s)

2nd most comm X-ALD

progressive

involves spinal cord and peripheral nerves then myelopathy/polyneuropathy and bladder dysfunc

symps: paraparesis, gait issues, leg stiffness/weakness, sphincter control, sexual dysfunc, may have adrenal insuff or cognitive/behavior issues

Addison’s disease w/o neurological involvement

addison’s= insuff cortisol and sometimes aldosterone from adrenal, more pronounced sympts under stress

primary adrenocortical insuff btwn 2yr and adult

no evidence neuro abnorm

increased very long chains

When to consider X-ALD?

1. boys w/ ADD and dementia, progress behavioral, vision loss, diff understanding spoken lang, worsening handwriting, incoord, or other neuro

2. young or middle-aged men w/ progress gait issues, leg stiff/weakness, sphincter control, and sexual dysfunc w/ or w/o adrenal insuff or cognitive/behavior

3. all males w/ primary adrenocortical insuff w/ or w/o neuro

4. adult women w/ progress paraparesis, abnorm sphincter control, and sensory disturb (mainly legs)

5. infants w/ positive NBS result

X-ALD diagnosis and geno-phenos

Brain MRI always abnorm in neuro symp males w/ cerebral disease, symm enhanced T2 signal

measurement very long chains sufficient in most males

ABCD1 seq an option

deletions assoc w/ milder pheno

certain missense changes assoc w/ severe

can’t predict pheno from very long chain levels

X-ALD treatment and prevention

adrenal steroid hormone therapy for every pt w/ adrenal cortical insuff!

all pts need ACTH stimulation test- detect adrenal failure

symptomatic for neuro sympts

prevention= stem cell transplant for those w/ minimal neuro findings and norm clinical neuro eval, NBS- a few states have added this

Potential problems w/ X-ALD on NBS

males- pheno varies from severe to adult onset and can’t predict pheno based on biochem or GT

females- uncover female carriers that are minors

uncover disorders like Zellweger which are not treatable

Organic Acidemias

inborn errors of metabolism

problem w/ step of AA catabolism (usually branched chain or lysine)

typically a dysfunc enzyme- AAs partially broken down until they reach dysfunctional one=detectable levels of organic acids in blood and urine or buildup of metabolites not norm found in body

1 in 1000 births- individually each acidemia is rare

sympts usually arise once baby is not in womb (begins its own metabolism)

15 on NBS in TX

typically AR

initial presentation is non-specific, eventually have metabolic crisis

typically fatal w/o tx

What conditions does initial presentation of organic acidemia look like?

sepsis

poor breastfeeding and neonatal asphyxia

clue could be prior death of sibling of pt

Signs of a metabolic crisis

hyperapnea, poor feeding-seizures, hypotonia, FTT, vomiting, lethargy, coma, death

Disease state

disorder of intoxication

accum of precursors behind block and lack after block

buildup of reactant can be processed thru diff pthwy that creates toxic metabolites

inability to generate energy

Early, acute presentation of organic acidemia

little to no func enzyme

clinical symp in 1st week

severe metabolic decompensation

Ongoing, intermittent presentation of organic acidemia

maintain some func of enzyme or diff pthwy has slightly compensated

present w/ acute episode of symp later in life after metabolic stressor

possible presentation= loss of intellectual func, DD, ataxia, recurrent ketoacidosis, psychiatric, seizures

Lab findings of organic acidemia

metabolic acidosis

high anion gap

ketosis

maybe hyperammonemia and hypoglycemia

neutropenia

increased lactate

Confirmatory testing of organic acidemia

NBS- positive=PCP screens symp, ACT sheet, consult metabolic specialist

if suspected need to get urine organic acids (takes 1-2 weeks, gives specific disorder), plasma AAs, and acylcarnitine profile

assay of deficient enzymes in lymphcytes

confirm w/ molecular testing- RR

familial variant testing

Treatment of organic acidemia

detect and treat early

keep levels of toxic metabolite low and avoid catabolism

acute metabolic decompensation= stop protein intake, promote anabolism w/ IV dextrose, and add compounds that increase disposal of metabolites

long-term= diet (low protein, formula w/o precursor AA, anabolic state), add compounds that increase disposal toxic metab, add cofactors to help existing func of dysfunc enzyme

Should you treat a pt w/ positive NBS and no clinical symptoms?

NO (other than galactosemia)

high rate false pos

protein restriction can be detrimental to norm infant

tx varies depending on disorder

Prognosis of organic acidemia

early detection and tx= very good long term outcome usually (avoid neuro probs w/ diet)

greater risk infection (depresses bone marrow)

increased risk pancreatitis

liver transplant

pregnancy w/ OAs= typically healthy preg, req strict monitoring of metabolic status during and post

Isovaleric Acidemia

defect in isovaleryl CoA dehydrogenase- OA disorder

IVD gene

symp= vomiting, ketosis, thrombocyto, maybe neuro and lethargy/coma/death, sweaty feet odor and microcephaly

could be asymp, can see acute and intermittent in same fam

dx= increase isovalerylglycine and 3-hydroxyisovaleric acids in urine and increased C5 and C5:C3 ratio on acylcarnitine profile

tx= acute- fluids and electrolytes (glucose, carnitine, glycine), long term-diet restrict leucine, provide carnitine and glycine

Propionic Acidemia

defect propionyl CoA carboxylase (biotin cofactor)

PCCA and PCCB

symp= dehydration, ketotic hyperglycinemia, maybe cognitive impair and DD w/ ultimately norm develop, chronic candidiasis, osetoporosis, abnorm ketogenesis

could be only neuro or asymp

dx= urine- propionic acid (inhibits urea cycle=hyperammonemia) and glycine, acylcarn-C3

tx= acute-fluids and electro, IV carnitine, anti-fungal to stop gut bact prod, longterm- protein restrict, carnitine

cardiomyopathy possible

Methylmalonic Acidemia

similar to propionic, ident clinically

defect methylmalonyl CoA mutase (enzyme) or adenosylcobalamin cofactor (could be due to B12 deficiency)

MUT, MMAA, MMAB genes

lesions in basal ganglia on MRI

dx= methylmalonic acid in urine and propionic acid

tx= acute-same as propionic, longterm-restrict protein, B12 (if cause of condition, could be all they need), carnitine, metronidazole, liver transplant

renal fail possible, late onset neuro disease, optic atrophy

Cobalamin C Disease

defect cobalamin metab=defects in both metylmalonyl CoA mutase and methionine synthase

MMACHC

sometimes progress neuro

other rarer types could lead to double pheno expression

symp= FTT, maybe dementia, DD, megaloblastic anemia, hypersegmented PMNs (problem w/ neutrophils), maybe thrombocyto

dx= homocystine and MMA in urine

tx= hydroxycobalamin injections (cobalamin precursor) and betaine

3-methylcrotonyl-CoA carboxylase deficiency (3-MCC)

most common OA

MCCC1 and MCCC2

symp= ketoacidosis, seizures, hypoglycemia, hyperammonemia→coma

could be asymp (positive NBS could actually be the mother)

dx= 3-hydroxyisovaleric acid much higher and 3-methylcrotonylglycine in urine, need acylcarnitine for dx

tx= no leucine, add carnitine

good prognosis, no ID

Glutaric Aciduria Type 1

defect glutaryl CoA dehydrogenase

GCDH gene, 1 in 300 in Manitoba Indians

symp= megalencephaly, macroceph, frontotemporal atrophy, increased caudate and putamen signal, lose milestones, rhabdomyolysis, subdural hematomas and retinal hemorrhage - mistaken for child abuse

onset= 14 months (earlier=increased risk death)

usually no metab decompensation

acute episodes resemble encephalopthy- recovery slow, DD, neuro

each episode=more degen

some pts never have episodes

dx= glutaric acid and 3-hydroxyglutaric acid in urine, rapid head growth, increase protein in CSF

tx= protein restrict, carnitine (diet doesn’t improve damage), NBS important!

Biotin Disorders

biotin= vitamin cofactor of carboxylases, not synth by humans

multiple carboxylase deficiency

Holocarboxylase Synthetase Deficiency

catalyses attach of biotin to apocarboxylase enzymes- activates carboxylase

HLCS

symp= dehydration, alopecia, rash on entire body, no neuro, immunodefi

can be fatal within few hrs of birth

dx=lactic acidemia, abnorm UOAs

tx=biotin- clears most symp

Biotinidase Deficiency

can’t extract biotin from diet or intestinal flora

BTD

symp= ataxia, skin rash, hearing and vision loss, DD, perioral stomatitis, alopecia

dx= abnorm UOAs, lactic acidosis, elevated lactate and pyruvate in CSF

tx= biotin-reverses most symp

Inborn errors of metabolism

specific enzyme deficien

normal pheno= 5-10% enzyme activity

enzymopathy= defective or absent enzyme

mostly AR

Amino Acidemias

AA can’t be metab

elevated levels of that AA

most AR

essential (not produced by body) and nonessential AAs

Classic Phenylketonuria (PKU)

1 in 10,000-15,000, most comm in caucasian>AAs>hispanic>Asian

norm until few months old- seizures, DD, behavior, psychiatric, musty/mouse-like odor, hypopigmen, eczema

PAH gene

majority compound heteros, north european founder effect

tx= low Phe diet, want under 6mg%, start in 1st mo and coninue for life, Kuvan=synth BH4, enzyme substitution allows for dietary freedom

during illness body catabolism increases Phe

untreated=develop perm ID

Types of PKU

normal= 2mg% or less Phe

classic (most comm)= 20mg% or more

hyperphe variant= 10-20mg%

benign persistent hyperphe= 4-10mg%

start diet only when confirmed (increased Phe:Tyr ratio)

treat 6mg% and above! (monitor 2-6mg% until they hit 6)

Maternal PKU

mother’s Phe level high= teratogen

ID, microceph, CHD, IUGR, low birth weight

prevention= strict diet to maintain maternal Phe under 6, supplement w/ Tyr during preg

Biopterin defects

1-2% of those w/ high Phe levels

high Phe:Tyr ratio and other similar symp

difficulty thermoreg and hypotonia

alters neurotransmitter levels

urine pterin analysis amd RBC DHPR assay

BH4 is cofactor for PAH

tx= CANNOT be treated w/ diet, Kuvan supplies BH4, prescription for neuro, early tx=healthy growth and develop

Tyrosinemia Type 1 (TYR1)

FAH gene

most severe

enzyme involved in breaking down Tyr, mut = increased succinylacetone and acid levels

Quebec founder effect

dx= increased Tyr, Met, and Phe, increased succinylacetone- pathognomonic if found in child w/ liver fail or severe renal disease, elevated Tyr metabolites in urine, increased urinary excretion delta-ALA, decreased FAH activity

Symptoms of Tyrosinemia Type 1 (TYR1)

neonate=usually asymp

1st few months=diarrhea, vomiting, fatigue, irritable, FTT, cabbage-like odor, increased bleeding

liver=enlarged liver, swollen legs, jaundice, increased liver cx

kidney=rickets, delays in walking

may also affect nervous sys

Treatment of Tyrosinemia Type 1 (TYR1)

Nitisinone/NTBC=inhibits 4-hydroxyphenylpyruvate dioxygenase (higher up in pthwy) =prevents liver and kidney damage=stops weakness and pain and may lessen carcinoma

low Tyr diet

Transient Neonatal Tyrosinemia

temporary inability to degrade Phe and Tyr

resolves as liver matures

seen in premature males

may cause mild DD and lang probs

Maple Syrup Urine Disease (MSUD)

more comm in old order mennonite pop

most comm form due to lack of branched-chain ketoacid dehydrogenase complex (BCKAD)- Leu, Ile, and Val not broken down

BCKDHA and B and DBT make up the subunits of BCKAD in mito

MSUD Clinical Classification

classic= neonatal-early child, poor feeding, apnea, siezure, hypoglycem, 0-2% BCKAD activ, death w/o tx to mild CNS impair

intermediate= infant-adult, ataxia, FTT, usually no acidosis, progress, 3-30%, severe psychomotor delay to norm

intermittent= child-adult, intermitt ataxia and ketoacidosis during infect or protein inget, 5-20%, death-normal

MSUD Metabolic Crisis

caused by hypoglycemia and toxic substance buildup in blood

1st symp=excess sleepiness, irritable, vomiting

other symp= poor appetite, infect, behavior, ataxia, maybe blindness

MSUD diagnosis and treatment

dx= maple syrup odor (12hrs after birth), high BCAAs (Leu, Ile, Val) and alloisoleucine=pathognomonic, abnorm branched hydroxyacids and ketoacids

tx= low BCAA diet w/ more starchy foods and fluids, Val and Ile supplem to decrease Leu, minor illness can cause crisis

Classical Homocystinuria (HCY)

more comm in Ireland

CBS norm breaks down methionine

blood buildup homocystine and methionine

CANT be dx via plasma AA or urine=homocystine/methionine panel required (increased levels)!

effects connective tiss- eye (ectopia lens, myopia), skeletal (osteoporosis, codfish vert, increased long bone length), CNS (ID and psychiatric), vascular system (occlusions), fair and brittle hair, thin skin, endocrine

Classical Homocystinuria (HCY) Treatment

low Met diet

maintain plasma homocystine <11micromol/L and total homocystine close to norm

supplements can prevent manifestations

lifelong tx=norm growth and intelligence

lowers chance vascular issue

some still develop ectopic lens

Urea Cycle purpose

degrade ammonia produced by protein catabolism to urea

Hyperammonemia

present in all urea cycle disorders except argininemia

high ammonia=affects brain and CNS

initial=poor appetite, fatigue, irritable, vomiting

left untreated= muscle weak, breathing, thermoreg, seizures, brain swell, coma and sometimes death

some have less severe symp or later on

need to find this to dx UCDs, molec GT helps distinguish them

N-acetylglutamate synthase deficiency (NAGS)

very rare

NAGS gene

mimics CPS deficiency

1st few days of life=hyperammonemia effects

some have less severe symp and some cant have high-protein food

may have episodes of ammonia toxicity

mitochondria

Carbamyl phosphate sythetase deficiency (CPS)

rare, more comm Japan

most severe UCD

CPS1

rapidly develop hyperammon as newborn

chronically at risk for repeated hyperammon- liver transplant

Ornithine transcarbamylase deficiency (OTC)

X-linked

progress liver damage, skin lesions, brittle hair

OTC gene

males have symp as severe as CPS defici

females=15% of carriers develop hyperammon (no hyperammon=executive func deficien)

Citrullinemia Type 1 (CIT)

ASS1

increased citrulline, urine orotic acid may be increased

hyperammon may be severe

tx slightly easier (waste nitrogen can be incorporated)

milder form can develop later child or adult less comm (headaches, partial blindness, ataxia, lethargy)

in cytosol

Citrullinemia Type 2 (CIT II)

primarily Japanese pop

SLC25A13- citrin= mito transporter of Asp/Glu, mut=reduced Asp avail for urea cycle

primarily effects nervous sys (confusion, restless, memory loss, abnorm behav, seizures)

liver enzymes, lactic acid, and bilirubin can be elevated

in cytosol

Citrullinemia Type 2 (CIT II) Other Presentations

neonatal intrahepatic cholestasis (NICCD): may develop CIT II feats, blocks bile flow, cant process certain nutrients, many cases resolve within year, may develop adult onset feats

adult-onset: life threatening- triggered by meds, infect, surgery, alcohol

Argininosuccinic Aciduria (ASA)

ASL

enzyme defect past when waste nitrogen can be incorporated

two forms= severe (infant) and milder (child)- DD, seizures, hepatomeg, skin and hair prob

increased citrulline and argininosuccinic acid

may have increased urine orotic acid

symp= possible rapid onset hyperammon as newborn and chronic liver enlarge and trichorrhexis nodosa (node-like appearing fragile hair)

cytoplasm

Argininemia (ARG)

very rare

ARG1

increased arginine and orotic acid

may have hyperammon

asymp neonate but hyperammon when receive diet protein

rarely has severe neonatal illness

often misdiagnosed as cerebral palsy

symp= 1-3yo, irritable, sleeping longer, hypotonia, microceph, hyperactive, delayed growth, DD, tremor, ataxia, etc

untreated=ID, seizures, spastic diplegia

Urea cycle disorder treatments

acute severe hyperammon= dialysis and hemofiltration to reduce ammon, IV or oral arginine hydrochloride and nitrogen scanvenger drugs to create alternative pthwy to excrete excess nitro

arginine supp for CIT II and ASA

Transcripts

mutiple per gene due to diff isoforms

MANE transcript= matched annotation from NCBI and EMBL-EBI=most bio relevant transcript

Substitutions

missense=change AA

nonsense= premature stop, * or Ter for termination or Stp for stop

synonymous= silent, no change AA, = or V