Passion to Compassion: Genomic Analysis-VCF-Format

Adressing the scenerio of 05 years old girl called Fatima:

Fatima is 05 years old and has been diagnosed with Phenylketonuria since birth. She has demonstrated complex responses to multiple medications and have multiple clinical conditions that are not explained by the disease variant or by 1 year of traditional diagnostic testing.

Phenylketonuria (PKU) is one of the common of the 300 inherited metabolic disorders. It caused by the deficiency of phenylalanine hydroxylase (PAH) enzyme in liver or rarely absence of a cofactor, tetrahydrobiopterin (BH4), as a result the essential amino acid phenylalanine is not metabolized in tyrosine. The blood levels are high in phenylalanine which is broken down into phenylketones especially phenylpyruvate which is excreted in urine and gives it a musty odor. If undiagnosed or untreated high blood level of phenylalanine can lead to the infant’s brain damage, intellectual abnormalities, seizures, microcephaly, and skin rashes by the end of first year of life.

PKU is an autosomal recessive condition, therefore, in order to have a clinical presentation the person has to be homozygous for the allelic variant, if a person has only one allele present the person is the carrier for the condition. PKU is commonly included in newborn screening panel in USA, Canada, many countries in Europe, Australia, New Zealand, Japan, Taiwan, South Korea, and Philippines etc. The PKU screening has not been established in Hong Kong, and India/Pakistan/Bangladesh/Indonesia. Thus less than 15% of the total newborns are tested for PKU around the world. The blood from the heel of the baby is taken for the phenylalanine assay.

PKU is classified under 04 phenotypes. The blood levels of phenylalanine (Phe) of patients with classical PKU is >1200 (μmol/L), atypical or mild PKU Phe levels 600-1200 (μmol/L) in benign hyperphenylalaninemia Phe level 200-600(μmol/L) and lastly Biopterin deficiency variable.

Higher degrees of consanguinity in Middle East can lead to the genetic disorders in offspring’s. The comprehensive analysis of genotypes and phenotypes lasting for 02 years study of 27 Kurdish patients born with PKU showed specific mutations in PAH gene among these patients prevalent in the ethnical area. Consanguinity was positive in 85% of marriages. All except one were not diagnosed with PKU at birth due to the absence of the PKU screening test at birth.

In classical PKU there is defective functioning of PAH enzyme in liver. The genetics of BH4 is complex and more than one enzymes are involved, malfunctioning of BH4 enzymes produce the biopterin deficiency variants.

Genotypes of PAH deficiency:

Majority of defects in 500 allelic variants range from defects as missense mutations, non-sense, splice site, silent, frame shift, larger deletions and insertions may occur. It is crucial to have a good control of Phenylalanine during pregnancy, as untreated maternal PKU (MPKU) can lead to severe fetal deformities. MPKU embryopathy, resembling fetal alcohol syndrome, include microcephaly, mental retardation, congenital heart disease, intrauterine growth retardation, facial deformities.
The mainstay of treatment in PKU is dietary restriction of Phenylalanine.

Whole genome sequencing/ Whole exome sequencing is especially useful in patients with congenital disorders especially if the consanguinity is presented (Berg et al., 2012).

Fatima’s who is 05 year old has PKU since birth, her parents are first cousins, she has been having complex pattern of illness which is not responsive to the general management of diet restriction rich in Phenylalanine all the genetic variants needs to be evaluated to see if they are the distinctive features of another congenital disorder associated with PKU.

Since Fatima has demonstrated complex clinical conditions and responses to medication their whole genome sequencing/whole exome sequencing provider (WGS/WES) provider should be notified with the situation so that the due attention is paid to the incidental findings of genetic variants and label them a potential disease causing mutation (DM) before labeling them as likely polymorphism or variants of uncertain significance (VUS). The DM variants in Fatima’s case need to be reviewed manually and less stringent filtering criteria should be used and applied to remove the majority of missense mutations need to be re-evaluated. The provider should not exclude the novel missense mutations, synonymous and non-coding variations in the genome sequencing evaluation.

The exome sequencing is a powerful and cost-effective tool of investigating the congenital conditions that effect the protein coding region of the human genetic code(Bamshad et al., 2011).

Reference:

Alibakhshi, R., Moradi, K., Mohebbi, Z., & Ghadiri, K. (2014). Mutation analysis of PAH gene in patients with PKU in western Iran and its association with polymorphisms: identification of four novel mutations. Metabolic Brain Disease, 29(1), 131–138.

Berg, J. S., Adams, M., Nassar, N., Bizon, C., Lee, K., Schmitt, C. P., … Evans, J. P. (2012). An informatics approach to analyzing the incidentalome. Genetics in Medicine, 15(1), 36–44.

Bick, D., & Dimmock, D. (2011). Whole exome and whole genome sequencing. Current Opinion in Pediatrics, 23(6), 594–600.

Centerwall, S. A., & Centerwall, W. R. (2000). The discovery of phenylketonuria: the story of a young couple, two retarded children, and a scientist. Pediatrics, 105(1), 89–103.

Hanley, W. B. (2012). Phenylketonuria (PKU)–A Success Story. Latest Findings in Intellectual and Developmental Disabilities Research. Retrieved from http://www.intechopen.com/source/pdfs/28170/InTech-Phenylketonuria_pku_a_success_story.pdf

Hanley, W. B. (2013). Phenylketonuria (PKU)-What Next? Mini-Review. J Genet Disor Genet Rep 2, 2, 2.

Wolf, S. M., Kahn, J. P., Lawrenz, F. P., & Nelson, C. A. (2006). The incidentalome. JAMA, 296(23), 2798–2802.

Some videos of patients with PKU;