Introduction

Typing of X chromosomal (ChrX) markers increasingly becomes an issue in kinship testing. Especially some special deficiency cases can be solved this way rather than by using autosomal and Y chromosomal (ChrY) markers [5] [6]. However, this applies only to a minority of kinship expertises. Consequently, only few scientists are dealing with this topic. Since the number of cases is low, the extent of important data is rising slowly. On the other hand, forensic certainty can be achieved only, when an expertise statement is founded on observations supplied by a solid base of data. Hence, it seems to be advisable to collect marker data such as allele distributions, null allele frequencies, mutations rates etc. in an online database accessible for the forensic community. Thus, studies of a limited extent may help to cumulate figures with a sufficient impact. Furthermore, if other scientific disciplines such as evolutionary anthropology will focus their attention also at ChrX markers, they would need reliable data for ChrX markers found in different ethnics all over the world. A worldwide survey of initial data regarding the variability of the markers may help to choose markers of interest. Due to the quite different inheritance mode, the ChrX typing can never achieve the same significance in this field as ChrY marker research has obtained. ChrX marker cluster haplotyping may nevertheless complete the well established disciplines of the haploid DNA marker research regarding ChrY and mitochondrial DNA. So, the success story of the database "YHRD - Y chromosome haplotype reference database” http://www.yhrd.org/index.html has encouraged us to start our project.

Finally, ChrX marker investigations may have a clinical significance. Although the whole human genome is sequenced now, there are reports that linkage analysis may help to identify disease genes [2]. Furthermore, some scientists dealing with oncology currently assemble marker panels for the investigation of microsatellite instability (MSI) and loss of heterozygosity (LOH). Nowadays in this context, they more and more consider also ChrX STRs [1] [3] [7].

Website architecture and data submitting procedure

ChrX marker localisation

ChrX typing in kinship testing requires a good knowledge about the linkage situation between the markers. Physical and genetic localisation of loci on the same chromosome are related, but unfortunately this relationship is not strictly linear. Since marker localisation is an important issue in ChrX-based kinship testing, the access to the special marker websites is guided via a ChrX ideogram or alternatively via a localisation table. While the ideogram provides an overview over the marker distribution on the chromosome, the localisation table figures physical and genetically localisation as exact as possible. Although the human genome has already been sequenced completely, the established human DNA databases do not provide exactly the same figures. However, we have observed that the Human Genome Browser of the Wellcome Trust Sanger Institute (http://www.ensembl.org/Homo_sapiens) and the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov) provide identical figures for nearly all loci, therefore we utilise this data. Our localisation table presents the physical locations of the STR as distance in bps from the Xp-telomere according to the databases mentioned.

The genetic localisation can be interpolated using mapped deCODE markers or using Rutgers combined linkage-physical human genome map (http://compgen.rutgers.edu/maps/).

All indications are given as distance from the ChrXp–telomere with centimorgan (cM) as unit.

Short accounts of ChrX markers

The descriptions of the STR markers are mainly based on papers published in printed forensic journals. They include a primer proposal for each marker but no complete PCR protocols. The amplicon lengths indicated refer to these primers. Allele designations are presented together with the typical repeat structures. To enable ladder calibration, the typing results are indicated for a set of reliable standard DNA i. e. K562, NA9947A, 9948 and NA3657 as recommended earlier [4]. Figures for DNA07 may follow in future.

Population data of STRs

Population data on ChrX STRs are collected from several papers. Although we considered mainly peer reviewed journals not all publications were suitable to provide data to our website. Unfortunately, nowadays an explanation on the ladder calibration method obviously seems to be no obligate presupposition for a paper on population data to be accepted. Hence, it can be seen that in some cases the published data did not meet the consensus allele nomenclature after the ISFG recommendation. In some cases, the situation is unclear. Such problems could be avoided if the authors would generally communicate the method of allele ladder calibration using at least 2 standard DNAs. Population genetic parameters such as mutation rates and PIC, PD, MEC etc, are also indicated, if already evaluated.

Population data regarding STR haplotypes

In males, the ChrX marker appears in hemizygous state. Hence, ChrX typing of marker clusters automatically provides haplotypes. Taking in account the crossing-over frequencies, which directly correlate to the genetic distances between the markers involved, such haplotypes can in certain pedigrees be used for kinship testing (instead of STR alleles). If two or more STR loci are used, the count of haplotypes may extend several hundreds or even more than thousand haplotypes. Since ChrX haplotyping may produce a large amount of data, not all data can be presented in printed journals. Therefore, complementary data publication beyond the printed basis paper may be useful. Our website offers the opportunity to publish such data online.

Submitting data for online publication

When starting this website, we ferreted out STR and haplotype data from literature and inserted the data into our web site by copying or transcribing. To facilitate the procedure in future, authors are requested to copy their published data in our web data sheet. Of course, unpublished data are also welcome.

These are the quality standards that have to be met:
Appropriate typing techniques has to be used. STRs with irregular alleles should always be typed using appropriate gene analyser equipment. In general at least two of the following standard DNAs have to be employed for ladder calibration: NA9948¹, NA9947², NA3657¹ and DNA07³. The DNA Standards can be purchased as indicated: Coriell Institute for Medical Research, Camden, NJ¹; Promega, Madison, WI²; Perkin Elmer, Foster City, CA³. Cell line DNA K562 is not sufficient for ladder calibration, especially when ChrX STRs are to be typed [4]. Some of the control DNAs recommended here are utilised in commercial profiling kits.

Observations on mutation rates should survey at least 50 meioses and have to be separated in maternal and paternal meiosis. The following population genetics parameters useful in forensic science should be calculated: MEC, PIC, HET, PDfemale, PDmale An appropriate calculation software is implemented on our website and can be used before submitting the data. Furthermore, the Hardy-Weinberg Equilibrium should be checked.

All over the world there are many countries that are settled by different ethnics. Therefore data should be addressed as precise as possible. We ask to name not only the country the population lives in is but to describe also the appropriate ethics (e.g. American Caucasians, Afro-Americans, Blackfoot Indians etc.).

In principle, the conditions mentioned for STRs also apply for haplotypes of STR clusters. However, the distance of the outermost markers of the whole cluster should not exceed a span of 5cM.

Concluding remarks

This website is operated by a loose connection of scientists linked by their interest in forensic ChrX research. The group has been founded by the authors of this article. We are not a corporate body. We try to operate this page with a high degree of care and scientific responsibility and intend to accept all submissions which are within the scope of this website and which meet the announced quality requirements. In some cases, reasons may exist to reject a submission. In such cases, the course of law is excluded. However, if the author is able to induce an intercession of an advisory board member of the Int J Legal Med or Forensic Sci Int the rejection may by evaluated again and possibly revised.

References

1. Buekers TE, Lallas TA, Buller RE (2000) Xp22.2-3 loss of heterozygosity is associated with germline BRCA1 mutation in ovarian cancer. Gynecol Oncol 76: 418-22.
2. Schurmann M, Reichel P, Muller-Myhsok B, Schlaak M, Muller-Quernheim J, Schwinger E (2001) Results from a genome-wide search for predisposing genes in sarcoidosis. Am J Respir Crit Care Med 164: 840-6.
3. Sood AK, Holmes R, Hendrix MJ, Buller RE (2001) Application of the National Cancer Institute international criteria for determination of microsatellite instability in ovarian cancer. Cancer Res 61: 4371-4.
4. Szibor R, Edelmann J, Hering S, Plate I, Wittig H, Roewer L, Wiegand P, Cali F, Romano V, Michael M (2003) Cell line DNA typing in forensic genetics--the necessity of reliable standards. Forensic Sci Int 138: 37-43.
5. Szibor R, Krawczak M, Hering S, Edelmann J, Kuhlisch E, Krause D (2003) Use of X-linked markers for forensic purposes. Int J Legal Med 117: 67-74.
6. Toni C, Presciuttini S, Spinetti I, Domenici R (2003) Population data of four X-chromosome markers in Tuscany, and their use in a deficiency paternity case. Forensic Sci Int 137: 215-6.
7. Vauhkonen H, Vauhkonen M, Sipponen P, Sajantila A (2004) Correlation between the allelic distribution of STRs in a Finnish population and phenotypically different gastrointestinal tumours: a study using four X-chromosomal markers (DXS7423, DXS8377, ARA, DXS101). Ann Hum Genet 68: 555-62.