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Haploid Autosomal Length (HAL) Calculator

Converts the physical portion of a chromosome arm into a percentage of the total autosomal genome

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Why use it

Required to feed data into viability models (like Cohen & Daniel) to predict reproductive outcomes for translocation carriers.

About

Essential for calculating the quantitative impact of chromosomal rearrangements. The tool converts the physical portion of an involved chromosome arm into a percentage of the total Haploid Autosomal Length (HAL). It includes both the classic Daniel (1985) proportions and updated hg38 genome assembly values. The total autosomal genome is 2,875 Mb (hg38).

When to use

  • Evaluating the size of deletions and duplications from a karyotype.
  • Calculating the unbalanced genomic load of adjacent-1 or adjacent-2 meiotic segregations.
  • Estimating the proportion of the genome affected by an inversion recombinant.
  • Translating cytogenetic band positions into approximate megabase and HAL percentages.

Formula

Segment HAL % = (Arm HAL %) × (Fraction of arm involved) Approximate Mb = Segment HAL % × 28.75

Pearls & pitfalls

  • 1% of HAL is roughly equivalent to 28.75 Megabases (Mb) of DNA (hg38: 2,875 Mb total autosomal).
  • Chromosome 1 is the largest, representing approximately 8.66% of the HAL (hg38), while Chromosome 21 represents about 1.62%.
  • Acrocentric chromosomes (13, 14, 15, 21, 22) have negligible p-arm euchromatin; p-arm values reflect satellite/stalk regions only.
  • This calculator can be used iteratively: calculate the monosomy segment and trisomy segment separately for a given translocation, then feed both values into the Viability Calculator.
  • The fraction can be estimated by measuring the segment on a chromosome ideogram with a ruler, or from molecular breakpoint positions.

Next steps

Use the resulting HAL percentage as the Monosomy or Trisomy input in the Cohen & Daniel Viability Calculator.

Evidence

Derived from standardized relative chromosome length measurements. Daniel A. (1985) original values and UCSC Genome Browser hg38 assembly (Gardner & Sutherland, Table A-1).

References

  1. Daniel A. The haploid autosomal length (HAL). Ann Hum Genet. 1985;49:265-271.
  2. Gardner RJM, Sutherland GR, Shaffer LG. Chromosome Abnormalities and Genetic Counseling. Table A-1.